Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/inputs/xcb Working: n-9-34.cluster.ucsf.bkslab.org:/scratch/xiaobo/83982/xcb-8058097.54 Result: /scratch/xiaobo/83982/xcb-8058097.54 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xcb 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/xak/inputs/xcb mkdir: created directory `/scratch/xiaobo/83982' mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54' /scratch/xiaobo/83982/xcb-8058097.54 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/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/83982/xcb-8058097.54/working' mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/protonate' Storing results in /scratch/xiaobo/83982/xcb-8058097.54/finished Working in /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 /scratch/xiaobo/83982/xcb-8058097.54/working/protonate /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Using inputs as protomers/tautomers. No processing done 444 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/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Bulk generating 3D conformations all protomers in /scratch/xiaobo/83982/xcb-8058097.54/working/3D mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/83982/xcb-8058097.54/working/protonate/xcb-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 ZINC001449695680 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building' mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449695680 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/1 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@]1(O)CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001449695680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449695680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001449695680 none O=C(NC[C@@]1(O)CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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, 5, 12, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 3, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 26, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 21, 21, 144, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4] 150 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 291 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/2 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@]1(O)CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001449695680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449695680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001449695680 none O=C(NC[C@@]1(O)CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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, 5, 12, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 3, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 26, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 4, 4, 2, 4, 4, 4, 5, 23, 23, 144, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4] 150 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 310 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001449695680 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/finished' Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680 Building ZINC001449695680 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449695680 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 1) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@]1(O)CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001449695680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449695680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001449695680 none O=C(NC[C@@]1(O)CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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, 5, 12, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 3, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 26, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 21, 21, 144, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4] 150 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 291 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 2) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@]1(O)CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001449695680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449695680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001449695680 none O=C(NC[C@@]1(O)CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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, 5, 12, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 3, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 26, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 4, 4, 2, 4, 4, 4, 5, 23, 23, 144, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4] 150 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 310 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001449695680 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449695680 Building ZINC001449895239 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449895239 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/3 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c1) `ZINC001449895239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449895239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001449895239 none Cc1csc(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', '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, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 24, 24, 24, 24, 24, 11, 11, 3, 1, 4, 4, 1, 1, 1, 1, 24] 50 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/4 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/4' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c1) `ZINC001449895239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449895239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001449895239 none Cc1csc(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', '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, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 24, 24, 24, 24, 24, 11, 11, 3, 1, 4, 4, 1, 1, 1, 1, 24] 50 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001449895239 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239 Building ZINC001449895239 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449895239 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 3) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c1) `ZINC001449895239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449895239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001449895239 none Cc1csc(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', '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, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 24, 24, 24, 24, 24, 11, 11, 3, 1, 4, 4, 1, 1, 1, 1, 24] 50 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 4) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c1) `ZINC001449895239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449895239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001449895239 none Cc1csc(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', '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, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 24, 24, 24, 24, 24, 11, 11, 3, 1, 4, 4, 1, 1, 1, 1, 24] 50 rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 18, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001449895239 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449895239 Building ZINC001449912757 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449912757 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/5 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3C[C@@H](C2)Cn2c(=O)cccc23)cn1) `ZINC001449912757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449912757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001449912757 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3C[C@@H](C2)Cn2c(=O)cccc23)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.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 11, 11, 11, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 11, 11, 20, 20, 20, 20, 20, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 11] 42 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/6 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3C[C@@H](C2)Cn2c(=O)cccc23)cn1) `ZINC001449912757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449912757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001449912757 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3C[C@@H](C2)Cn2c(=O)cccc23)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.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 10, 10, 10, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 48 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001449912757 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757 Building ZINC001449912757 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449912757 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 5) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H]3C[C@@H](C2)Cn2c(=O)cccc23)cn1) `ZINC001449912757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449912757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001449912757 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3C[C@@H](C2)Cn2c(=O)cccc23)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.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 11, 11, 11, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 11, 11, 20, 20, 20, 20, 20, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 11] 42 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 6) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2C[C@H]3C[C@@H](C2)Cn2c(=O)cccc23)cn1) `ZINC001449912757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449912757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001449912757 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H]3C[C@@H](C2)Cn2c(=O)cccc23)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.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 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, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 10, 10, 10, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 48 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001449912757 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449912757 Building ZINC001449971243 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449971243 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/7 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(C3CS(=O)(=O)C3)C2)cn1) `ZINC001449971243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449971243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001449971243 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(C3CS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 2, 4, 13, 13, 21, 26, 26, 26, 26, 26, 13, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 13, 13, 13, 26, 26, 26, 26, 26, 13, 13, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/8 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(C3CS(=O)(=O)C3)C2)cn1) `ZINC001449971243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449971243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001449971243 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(C3CS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 2, 4, 12, 12, 19, 27, 27, 27, 27, 27, 12, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 12, 12, 12, 27, 27, 27, 27, 27, 12, 12, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001449971243 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243 Building ZINC001449971243 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449971243 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 7) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(C3CS(=O)(=O)C3)C2)cn1) `ZINC001449971243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449971243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001449971243 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC(C3CS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 2, 4, 13, 13, 21, 26, 26, 26, 26, 26, 13, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 13, 13, 13, 26, 26, 26, 26, 26, 13, 13, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 8) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(C3CS(=O)(=O)C3)C2)cn1) `ZINC001449971243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449971243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001449971243 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC(C3CS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 2, 4, 12, 12, 19, 27, 27, 27, 27, 27, 12, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 12, 12, 12, 27, 27, 27, 27, 27, 12, 12, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001449971243 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001449971243 Building ZINC001450610935 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450610935 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/9 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)c2cn[nH]c2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001450610935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450610935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001450610935 none O=C(NC1CCN(C(=O)c2cn[nH]c2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 6, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 6, 23, 23, 23, 23, 47, 47, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 23, 23, 23, 23, 50, 50, 23, 23, 23, 23, 3, 3, 6, 3, 3] 100 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/10 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)c2cn[nH]c2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001450610935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450610935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001450610935 none O=C(NC1CCN(C(=O)c2cn[nH]c2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 6, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 6, 24, 24, 24, 24, 49, 49, 50, 50, 50, 50, 50, 24, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 23, 24, 24, 24, 24, 50, 50, 24, 24, 24, 24, 3, 3, 6, 3, 3] 100 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: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001450610935 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935 Building ZINC001450610935 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450610935 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 9) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)c2cn[nH]c2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001450610935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450610935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001450610935 none O=C(NC1CCN(C(=O)c2cn[nH]c2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 6, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 6, 23, 23, 23, 23, 47, 47, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 22, 23, 23, 23, 23, 50, 50, 23, 23, 23, 23, 3, 3, 6, 3, 3] 100 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 10) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)c2cn[nH]c2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001450610935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450610935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001450610935 none O=C(NC1CCN(C(=O)c2cn[nH]c2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 6, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 6, 24, 24, 24, 24, 49, 49, 50, 50, 50, 50, 50, 24, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 23, 24, 24, 24, 24, 50, 50, 24, 24, 24, 24, 3, 3, 6, 3, 3] 100 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: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001450610935 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450610935 Building ZINC001450726179 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450726179 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/11 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1ccc(OC)c(S(N)(=O)=O)c1) `ZINC001450726179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450726179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001450726179 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1ccc(OC)c(S(N)(=O)=O)c1 NO_LONG_NAME dock atom 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 7, 19, 19, 7, 7, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19] 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, 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/83982/xcb-8058097.54/working/building/ZINC001450726179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/12 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1ccc(OC)c(S(N)(=O)=O)c1) `ZINC001450726179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450726179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001450726179 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1ccc(OC)c(S(N)(=O)=O)c1 NO_LONG_NAME dock atom 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 7, 19, 19, 7, 7, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19] 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, 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/83982/xcb-8058097.54/working/building/ZINC001450726179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001450726179 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179 Building ZINC001450726179 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450726179 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 11) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1ccc(OC)c(S(N)(=O)=O)c1) `ZINC001450726179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450726179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001450726179 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1ccc(OC)c(S(N)(=O)=O)c1 NO_LONG_NAME dock atom 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 7, 19, 19, 7, 7, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19] 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, 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/83982/xcb-8058097.54/working/building/ZINC001450726179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 12) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1ccc(OC)c(S(N)(=O)=O)c1) `ZINC001450726179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450726179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001450726179 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1ccc(OC)c(S(N)(=O)=O)c1 NO_LONG_NAME dock atom 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 7, 19, 19, 7, 7, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19] 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, 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/83982/xcb-8058097.54/working/building/ZINC001450726179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001450726179 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450726179 Building ZINC001450808499 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450808499 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/13 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1n[nH]c(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)n1) `ZINC001450808499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450808499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001450808499 none Nc1n[nH]c(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)n1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 6, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 22, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 28, 28, 28, 26, 26, 22, 22, 6, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/14 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1n[nH]c(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)n1) `ZINC001450808499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450808499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001450808499 none Nc1n[nH]c(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)n1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 6, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 22, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 28, 28, 28, 26, 26, 22, 22, 6, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001450808499 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499 Building ZINC001450808499 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450808499 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 13) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1n[nH]c(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)n1) `ZINC001450808499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450808499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001450808499 none Nc1n[nH]c(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)n1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 6, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 22, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 28, 28, 28, 26, 26, 22, 22, 6, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 14) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1n[nH]c(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)n1) `ZINC001450808499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450808499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001450808499 none Nc1n[nH]c(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)n1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 6, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 22, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 28, 28, 28, 26, 26, 22, 22, 6, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001450808499 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450808499 Building ZINC001450961570 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450961570 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/15 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC(=O)Nc2ncccc2C)cn1) `ZINC001450961570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450961570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001450961570 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC(=O)Nc2ncccc2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 1, 8, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 6, 18, 18, 19, 26, 26, 26, 26, 26, 26, 4, 4, 9, 9, 9, 9, 9, 4, 2, 4, 4, 6, 6, 19, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/16 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCC(=O)Nc2ncccc2C)cn1) `ZINC001450961570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450961570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001450961570 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCC(=O)Nc2ncccc2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 1, 8, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 6, 17, 17, 18, 25, 25, 25, 25, 25, 25, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 4, 6, 6, 18, 25, 25, 25, 25, 25, 25, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001450961570 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570 Building ZINC001450961570 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450961570 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 15) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCCC(=O)Nc2ncccc2C)cn1) `ZINC001450961570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450961570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001450961570 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCC(=O)Nc2ncccc2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 1, 8, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 6, 18, 18, 19, 26, 26, 26, 26, 26, 26, 4, 4, 9, 9, 9, 9, 9, 4, 2, 4, 4, 6, 6, 19, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 16) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCCC(=O)Nc2ncccc2C)cn1) `ZINC001450961570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450961570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001450961570 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCC(=O)Nc2ncccc2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 1, 8, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 6, 17, 17, 18, 25, 25, 25, 25, 25, 25, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 4, 6, 6, 18, 25, 25, 25, 25, 25, 25, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001450961570 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001450961570 Building ZINC001451066920 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451066920 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/17 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)Cn2ccnn2)cc1Cl) `ZINC001451066920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451066920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001451066920 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)Cn2ccnn2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 13, 13, 13, 22, 26, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 4, 9, 9, 39, 22, 22, 26, 26, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/18 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](O)Cn2ccnn2)cc1Cl) `ZINC001451066920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451066920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001451066920 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](O)Cn2ccnn2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 11, 11, 11, 20, 25, 25, 25, 25, 6, 6, 6, 12, 12, 12, 6, 6, 3, 7, 7, 33, 20, 20, 25, 25, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451066920 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920 Building ZINC001451066920 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451066920 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 17) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)Cn2ccnn2)cc1Cl) `ZINC001451066920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451066920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001451066920 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)Cn2ccnn2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 13, 13, 13, 22, 26, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 4, 9, 9, 39, 22, 22, 26, 26, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 18) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](O)Cn2ccnn2)cc1Cl) `ZINC001451066920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451066920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001451066920 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](O)Cn2ccnn2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 11, 11, 11, 20, 25, 25, 25, 25, 6, 6, 6, 12, 12, 12, 6, 6, 3, 7, 7, 33, 20, 20, 25, 25, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451066920 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066920 Building ZINC001451066929 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451066929 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/19 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)Cn2ccnn2)cc1Cl) `ZINC001451066929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451066929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001451066929 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)Cn2ccnn2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 11, 11, 11, 21, 24, 24, 24, 24, 6, 6, 6, 12, 12, 12, 6, 6, 3, 7, 7, 33, 21, 21, 24, 24, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/20 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)Cn2ccnn2)cc1Cl) `ZINC001451066929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451066929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001451066929 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)Cn2ccnn2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 13, 13, 13, 22, 26, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 4, 9, 9, 39, 22, 22, 26, 26, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451066929 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929 Building ZINC001451066929 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451066929 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 19) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)Cn2ccnn2)cc1Cl) `ZINC001451066929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451066929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001451066929 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)Cn2ccnn2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 11, 11, 11, 21, 24, 24, 24, 24, 6, 6, 6, 12, 12, 12, 6, 6, 3, 7, 7, 33, 21, 21, 24, 24, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 20) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)Cn2ccnn2)cc1Cl) `ZINC001451066929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451066929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001451066929 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)Cn2ccnn2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 1, 8, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 13, 13, 13, 22, 26, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 4, 9, 9, 39, 22, 22, 26, 26, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451066929 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451066929 Building ZINC001451242961 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451242961 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/21 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)[C@H]1COCC12OCCO2) `ZINC001451242961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451242961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451242961 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)[C@H]1COCC12OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 20, 34, 32, 36, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 4, 20, 20, 36, 36, 36, 36, 36, 36, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 208 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/22 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)[C@H]1COCC12OCCO2) `ZINC001451242961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451242961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451242961 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)[C@H]1COCC12OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 17, 32, 34, 35, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 4, 17, 17, 35, 35, 35, 35, 35, 35, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451242961 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961 Building ZINC001451242961 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451242961 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 21) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC(C)(C)[C@H]1COCC12OCCO2) `ZINC001451242961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451242961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451242961 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)[C@H]1COCC12OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 20, 34, 32, 36, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 4, 20, 20, 36, 36, 36, 36, 36, 36, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 208 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 22) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC(C)(C)[C@H]1COCC12OCCO2) `ZINC001451242961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451242961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451242961 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)[C@H]1COCC12OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 17, 32, 34, 35, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 4, 17, 17, 35, 35, 35, 35, 35, 35, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451242961 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242961 Building ZINC001451242979 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451242979 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/23 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)[C@@H]1COCC12OCCO2) `ZINC001451242979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451242979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451242979 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)[C@@H]1COCC12OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 17, 32, 34, 35, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 4, 17, 17, 35, 35, 35, 35, 35, 35, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/24 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)[C@@H]1COCC12OCCO2) `ZINC001451242979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451242979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451242979 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)[C@@H]1COCC12OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 20, 32, 34, 36, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 4, 20, 20, 36, 36, 36, 36, 36, 36, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 208 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451242979 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979 Building ZINC001451242979 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451242979 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 23) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC(C)(C)[C@@H]1COCC12OCCO2) `ZINC001451242979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451242979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451242979 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)[C@@H]1COCC12OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 17, 32, 34, 35, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 4, 17, 17, 35, 35, 35, 35, 35, 35, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 24) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC(C)(C)[C@@H]1COCC12OCCO2) `ZINC001451242979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451242979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451242979 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)[C@@H]1COCC12OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 20, 32, 34, 36, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 4, 20, 20, 36, 36, 36, 36, 36, 36, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 208 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451242979 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451242979 Building ZINC001451447886 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451447886 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/25 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC001451447886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451447886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001451447886 none CNC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 15, 23, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 6, 6, 29, 29, 29, 29, 15, 6, 6, 6, 6, 6, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/26 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC001451447886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451447886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001451447886 none CNC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 12, 19, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 4, 4, 28, 28, 28, 28, 12, 4, 4, 4, 4, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 121 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451447886 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886 Building ZINC001451447886 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451447886 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 25) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC001451447886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451447886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001451447886 none CNC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 15, 23, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 6, 6, 29, 29, 29, 29, 15, 6, 6, 6, 6, 6, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 125 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 26) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC001451447886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451447886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001451447886 none CNC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 12, 19, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 4, 4, 28, 28, 28, 28, 12, 4, 4, 4, 4, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 121 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451447886 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451447886 Building ZINC001451840182 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451840182 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/27 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2O[C@H]2CC(=O)N2)cn1) `ZINC001451840182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451840182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001451840182 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2O[C@H]2CC(=O)N2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 7, 7, 7, 13, 20, 20, 20, 20, 20, 6, 6, 12, 12, 12, 12, 12, 6, 2, 7, 7, 7, 7, 20, 20, 20, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/28 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/28' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2O[C@H]2CC(=O)N2)cn1) `ZINC001451840182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451840182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001451840182 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2O[C@H]2CC(=O)N2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 13, 20, 20, 20, 20, 20, 6, 6, 12, 12, 12, 12, 12, 6, 3, 7, 7, 7, 7, 20, 20, 20, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451840182 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182 Building ZINC001451840182 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451840182 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 27) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2ccccc2O[C@H]2CC(=O)N2)cn1) `ZINC001451840182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451840182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001451840182 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2O[C@H]2CC(=O)N2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 7, 7, 7, 13, 20, 20, 20, 20, 20, 6, 6, 12, 12, 12, 12, 12, 6, 2, 7, 7, 7, 7, 20, 20, 20, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 28) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2ccccc2O[C@H]2CC(=O)N2)cn1) `ZINC001451840182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451840182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001451840182 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2O[C@H]2CC(=O)N2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 7, 7, 7, 13, 20, 20, 20, 20, 20, 6, 6, 12, 12, 12, 12, 12, 6, 3, 7, 7, 7, 7, 20, 20, 20, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451840182 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840182 Building ZINC001451840191 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451840191 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/29 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2O[C@@H]2CC(=O)N2)cn1) `ZINC001451840191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451840191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001451840191 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2O[C@@H]2CC(=O)N2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 14, 21, 21, 21, 21, 21, 6, 6, 12, 12, 12, 12, 12, 6, 3, 7, 7, 7, 7, 21, 21, 21, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/30 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2O[C@@H]2CC(=O)N2)cn1) `ZINC001451840191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451840191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001451840191 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2O[C@@H]2CC(=O)N2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 4, 7, 7, 7, 13, 19, 19, 19, 19, 19, 6, 6, 12, 12, 12, 12, 12, 6, 2, 7, 7, 7, 7, 19, 19, 19, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451840191 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191 Building ZINC001451840191 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451840191 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 29) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/29: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2ccccc2O[C@@H]2CC(=O)N2)cn1) `ZINC001451840191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451840191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001451840191 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2O[C@@H]2CC(=O)N2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 14, 21, 21, 21, 21, 21, 6, 6, 12, 12, 12, 12, 12, 6, 3, 7, 7, 7, 7, 21, 21, 21, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 30) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2ccccc2O[C@@H]2CC(=O)N2)cn1) `ZINC001451840191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451840191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001451840191 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2O[C@@H]2CC(=O)N2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 4, 7, 7, 7, 13, 19, 19, 19, 19, 19, 6, 6, 12, 12, 12, 12, 12, 6, 2, 7, 7, 7, 7, 19, 19, 19, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001451840191 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001451840191 Building ZINC001452116514 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452116514 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/31 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCn1cnccc1=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001452116514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452116514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001452116514 none O=C(NCCn1cnccc1=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 17, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 17, 17, 25, 25, 25, 25, 25, 7, 7, 7, 7] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/32 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCn1cnccc1=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001452116514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452116514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001452116514 none O=C(NCCn1cnccc1=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 17, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 17, 17, 25, 25, 25, 25, 25, 7, 7, 7, 7] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001452116514 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514 Building ZINC001452116514 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452116514 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 31) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCn1cnccc1=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001452116514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452116514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001452116514 none O=C(NCCn1cnccc1=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 17, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 17, 17, 25, 25, 25, 25, 25, 7, 7, 7, 7] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 32) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCn1cnccc1=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001452116514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452116514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001452116514 none O=C(NCCn1cnccc1=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 17, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 17, 17, 25, 25, 25, 25, 25, 7, 7, 7, 7] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001452116514 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452116514 Building ZINC001452230346 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452230346 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/33 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)N1CCOCC1) `ZINC001452230346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452230346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001452230346 none CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 6, 18, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 18, 35, 36, 45, 45, 45, 45, 45, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 4, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 183 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/34 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)N1CCOCC1) `ZINC001452230346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452230346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001452230346 none CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 13, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 30, 30, 40, 40, 40, 40, 40, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 172 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001452230346 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346 Building ZINC001452230346 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452230346 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 33) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)N1CCOCC1) `ZINC001452230346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452230346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001452230346 none CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 6, 18, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 18, 35, 36, 45, 45, 45, 45, 45, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 4, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 183 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 34) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)N1CCOCC1) `ZINC001452230346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452230346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001452230346 none CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 13, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 30, 30, 40, 40, 40, 40, 40, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 172 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001452230346 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452230346 Building ZINC001452558969 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452558969 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/35 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2nnc(O)n2C2CC2)cn1) `ZINC001452558969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452558969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001452558969 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2nnc(O)n2C2CC2)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.2', 'N.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 12, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 29, 29, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 13, 13, 66, 29, 29, 29, 29, 29, 6] 150 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]) total number of confs: 185 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/36 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2nnc(O)n2C2CC2)cn1) `ZINC001452558969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452558969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001452558969 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2nnc(O)n2C2CC2)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.2', 'N.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 12, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 30, 30, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 13, 13, 63, 30, 30, 30, 30, 30, 6] 150 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]) total number of confs: 190 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001452558969 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969 Building ZINC001452558969 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452558969 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 35) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCc2nnc(O)n2C2CC2)cn1) `ZINC001452558969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452558969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001452558969 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2nnc(O)n2C2CC2)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.2', 'N.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 12, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 29, 29, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 13, 13, 66, 29, 29, 29, 29, 29, 6] 150 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]) total number of confs: 185 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 36) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCc2nnc(O)n2C2CC2)cn1) `ZINC001452558969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452558969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001452558969 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2nnc(O)n2C2CC2)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.2', 'N.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 12, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 30, 30, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 13, 13, 63, 30, 30, 30, 30, 30, 6] 150 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]) total number of confs: 190 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001452558969 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452558969 Building ZINC001452983525 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452983525 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/37 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1) `ZINC001452983525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452983525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001452983525 none NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 12, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 20, 30, 10, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 30, 30, 5, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/38 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1) `ZINC001452983525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452983525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001452983525 none NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 12, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 30, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 30, 30, 5, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001452983525 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525 Building ZINC001452983525 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452983525 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 37) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1) `ZINC001452983525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452983525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001452983525 none NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 12, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 20, 30, 10, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 30, 30, 5, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 38) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1) `ZINC001452983525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452983525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001452983525 none NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 12, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 30, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 30, 30, 5, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001452983525 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001452983525 Building ZINC001546047321 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001546047321 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/39 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 36, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/40 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 33, 33, 33, 33, 35, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 4, 4, 2, 2, 4, 4, 4, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 33, 33, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/41 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/41' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 36, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/42 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/42' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 33, 33, 33, 33, 35, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 4, 4, 2, 2, 4, 4, 4, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 33, 33, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001546047321 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 Building ZINC001546047321 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001546047321 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 39) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 36, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 40) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 33, 33, 33, 33, 35, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 4, 4, 2, 2, 4, 4, 4, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 33, 33, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 41) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 36, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 42) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 33, 33, 33, 33, 35, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 4, 4, 2, 2, 4, 4, 4, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 33, 33, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001546047321 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 Building ZINC001546047321 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001546047321 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 39) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 36, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 40) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 33, 33, 33, 33, 35, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 4, 4, 2, 2, 4, 4, 4, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 33, 33, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 41) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 36, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 42) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 33, 33, 33, 33, 35, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 4, 4, 2, 2, 4, 4, 4, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 33, 33, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001546047321 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 Building ZINC001546047321 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001546047321 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 39) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 36, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 40) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 33, 33, 33, 33, 35, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 4, 4, 2, 2, 4, 4, 4, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 33, 33, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 41) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 36, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 42) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001546047321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047321 none O=C(N[C@H]1CC[N@@]([C@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 33, 33, 33, 33, 35, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 4, 4, 2, 2, 4, 4, 4, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 33, 33, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001546047321 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047321 Building ZINC001546047322 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001546047322 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/43 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 8, 34, 34, 34, 34, 35, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/44 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 35, 49, 49, 49, 49, 49, 49, 34, 34, 1, 1, 1, 5, 5, 1, 5, 5, 5, 4, 34, 34, 34, 34, 49, 49, 49, 49, 34, 34, 34, 34, 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: 149 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/45 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/45' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 8, 34, 34, 34, 34, 35, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/46 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/46' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 35, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001546047322 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 Building ZINC001546047322 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001546047322 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 43) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 8, 34, 34, 34, 34, 35, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 44) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 35, 49, 49, 49, 49, 49, 49, 34, 34, 1, 1, 1, 5, 5, 1, 5, 5, 5, 4, 34, 34, 34, 34, 49, 49, 49, 49, 34, 34, 34, 34, 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: 149 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 45) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 8, 34, 34, 34, 34, 35, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 46) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 35, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001546047322 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 Building ZINC001546047322 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001546047322 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 43) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 8, 34, 34, 34, 34, 35, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 44) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 35, 49, 49, 49, 49, 49, 49, 34, 34, 1, 1, 1, 5, 5, 1, 5, 5, 5, 4, 34, 34, 34, 34, 49, 49, 49, 49, 34, 34, 34, 34, 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: 149 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 45) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 8, 34, 34, 34, 34, 35, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 46) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 35, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001546047322 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 Building ZINC001546047322 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001546047322 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 43) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 8, 34, 34, 34, 34, 35, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 44) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 35, 49, 49, 49, 49, 49, 49, 34, 34, 1, 1, 1, 5, 5, 1, 5, 5, 5, 4, 34, 34, 34, 34, 49, 49, 49, 49, 34, 34, 34, 34, 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: 149 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 45) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 8, 34, 34, 34, 34, 35, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 46) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001546047322.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001546047322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001546047322 none O=C(N[C@H]1CC[N@@]([C@@H]2CCOC2=O)CC1)[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', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 12, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 8, 10, 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, 7, 34, 34, 34, 34, 35, 50, 50, 50, 50, 50, 50, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001546047322 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546047322 Building ZINC001453507679 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453507679 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/47 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC(n3cc(C(N)=O)nn3)CC2)c1) `ZINC001453507679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453507679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001453507679 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC(n3cc(C(N)=O)nn3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 8, 11, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 24, 24, 24, 26, 26, 24, 24, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 24, 26, 26, 8, 8, 8, 8, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/48 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC(n3cc(C(N)=O)nn3)CC2)c1) `ZINC001453507679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453507679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001453507679 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC(n3cc(C(N)=O)nn3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 8, 11, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 5, 6, 7, 7, 7, 7, 21, 21, 21, 26, 26, 21, 21, 7, 7, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 21, 26, 26, 7, 7, 7, 7, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001453507679 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679 Building ZINC001453507679 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453507679 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 47) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC(n3cc(C(N)=O)nn3)CC2)c1) `ZINC001453507679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453507679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001453507679 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC(n3cc(C(N)=O)nn3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 8, 11, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 24, 24, 24, 26, 26, 24, 24, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 24, 26, 26, 8, 8, 8, 8, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 48) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/48: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC(n3cc(C(N)=O)nn3)CC2)c1) `ZINC001453507679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453507679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001453507679 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC(n3cc(C(N)=O)nn3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 8, 11, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 5, 6, 7, 7, 7, 7, 21, 21, 21, 26, 26, 21, 21, 7, 7, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 21, 26, 26, 7, 7, 7, 7, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001453507679 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453507679 Building ZINC001453881417 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453881417 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/49 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nccn2c1) `ZINC001453881417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453881417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001453881417 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nccn2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 15, 15, 5, 2, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/50 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2nccn2c1) `ZINC001453881417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453881417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001453881417 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2nccn2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 15, 15, 5, 2, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001453881417 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417 Building ZINC001453881417 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453881417 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 49) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/49: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nccn2c1) `ZINC001453881417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453881417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001453881417 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nccn2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 15, 15, 5, 2, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 50) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2nccn2c1) `ZINC001453881417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453881417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001453881417 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2nccn2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 15, 15, 5, 2, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001453881417 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001453881417 Building ZINC001454268536 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454268536 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/51 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@H](C)O) `ZINC001454268536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454268536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268536 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 6, 6, 6, 18, 38, 38, 38, 43, 43, 43, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 6, 18, 18, 114, 43, 43, 43, 129] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 451 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/52 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@H](C)O) `ZINC001454268536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454268536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268536 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 5, 20, 35, 35, 35, 38, 38, 38, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 5, 20, 20, 105, 38, 38, 38, 114] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 404 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454268536 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536 Building ZINC001454268536 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454268536 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 51) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@H](C)O) `ZINC001454268536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454268536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268536 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 6, 6, 6, 18, 38, 38, 38, 43, 43, 43, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 6, 18, 18, 114, 43, 43, 43, 129] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 451 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 52) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@H](C)O) `ZINC001454268536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454268536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268536 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 5, 20, 35, 35, 35, 38, 38, 38, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 5, 20, 20, 105, 38, 38, 38, 114] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 404 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454268536 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268536 Building ZINC001454268571 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454268571 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/53 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)[C@H](C)O) `ZINC001454268571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454268571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268571 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 5, 5, 5, 19, 43, 43, 40, 43, 44, 44, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 5, 19, 19, 129, 44, 44, 44, 132] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 474 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/54 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)[C@H](C)O) `ZINC001454268571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454268571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268571 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 18, 43, 43, 40, 41, 43, 43, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 18, 18, 129, 43, 43, 43, 129] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 472 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454268571 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571 Building ZINC001454268571 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454268571 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 53) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)[C@H](C)O) `ZINC001454268571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454268571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268571 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 5, 5, 5, 19, 43, 43, 40, 43, 44, 44, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 5, 19, 19, 129, 44, 44, 44, 132] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 474 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 54) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)[C@H](C)O) `ZINC001454268571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454268571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268571 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 18, 43, 43, 40, 41, 43, 43, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 18, 18, 129, 43, 43, 43, 129] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 472 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454268571 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268571 Building ZINC001454268574 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454268574 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/55 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)[C@@H](C)O) `ZINC001454268574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454268574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268574 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 6, 6, 6, 22, 35, 35, 35, 39, 39, 39, 4, 4, 4, 9, 9, 8, 9, 9, 4, 4, 4, 6, 22, 22, 105, 39, 39, 39, 117] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 422 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/56 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)[C@@H](C)O) `ZINC001454268574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454268574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268574 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 6, 6, 6, 18, 38, 38, 38, 43, 43, 43, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 6, 18, 18, 114, 43, 43, 43, 129] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 450 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454268574 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574 Building ZINC001454268574 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454268574 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 55) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)[C@@H](C)O) `ZINC001454268574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454268574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268574 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 6, 6, 6, 22, 35, 35, 35, 39, 39, 39, 4, 4, 4, 9, 9, 8, 9, 9, 4, 4, 4, 6, 22, 22, 105, 39, 39, 39, 117] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 422 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 56) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)[C@@H](C)O) `ZINC001454268574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454268574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268574 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 6, 6, 6, 18, 38, 38, 38, 43, 43, 43, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 6, 18, 18, 114, 43, 43, 43, 129] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 450 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454268574 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268574 Building ZINC001454268577 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454268577 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/57 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@@H](C)O) `ZINC001454268577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454268577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268577 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 20, 43, 43, 39, 42, 44, 44, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 20, 20, 129, 44, 44, 44, 132] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 474 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/58 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@@H](C)O) `ZINC001454268577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454268577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268577 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 25, 25, 25, 38, 37, 38, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 3, 13, 13, 75, 37, 38, 38, 114] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 392 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454268577 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577 Building ZINC001454268577 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454268577 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 57) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@@H](C)O) `ZINC001454268577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454268577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268577 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 20, 43, 43, 39, 42, 44, 44, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 20, 20, 129, 44, 44, 44, 132] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 474 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 58) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@@H](C)O) `ZINC001454268577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454268577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001454268577 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 25, 25, 25, 38, 37, 38, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 3, 13, 13, 75, 37, 38, 38, 114] 450 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 392 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454268577 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454268577 Building ZINC001454463784 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454463784 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/59 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC=CC12CCCC2) `ZINC001454463784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454463784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001454463784 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC=CC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.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, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 19, 19, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/60 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/60' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC=CC12CCCC2) `ZINC001454463784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454463784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001454463784 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC=CC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.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, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 18, 18, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454463784 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784 Building ZINC001454463784 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454463784 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 59) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC=CC12CCCC2) `ZINC001454463784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454463784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001454463784 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC=CC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.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, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 19, 19, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 60) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC=CC12CCCC2) `ZINC001454463784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454463784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001454463784 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC=CC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.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, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 18, 18, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454463784 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454463784 Building ZINC001454534265 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454534265 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/61 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cc2cnccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001454534265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454534265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001454534265 none C[C@@H]1Cc2cnccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 3, 12, 12, 3, 3, 3, 3] 33 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/62 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cc2cnccc2N1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001454534265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454534265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001454534265 none C[C@@H]1Cc2cnccc2N1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 6, 6, 6, 6] 45 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454534265 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265 Building ZINC001454534265 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454534265 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 61) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1Cc2cnccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001454534265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454534265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001454534265 none C[C@@H]1Cc2cnccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 3, 12, 12, 3, 3, 3, 3] 33 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 62) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1Cc2cnccc2N1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001454534265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454534265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001454534265 none C[C@@H]1Cc2cnccc2N1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 6, 6, 6, 6] 45 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454534265 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534265 Building ZINC001454534266 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454534266 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/63 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cc2cnccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001454534266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454534266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001454534266 none C[C@H]1Cc2cnccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 6, 6, 6, 6] 46 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/64 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/64' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cc2cnccc2N1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001454534266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454534266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001454534266 none C[C@H]1Cc2cnccc2N1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 3, 12, 12, 3, 3, 3, 3] 33 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454534266 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266 Building ZINC001454534266 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454534266 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 63) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1Cc2cnccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001454534266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454534266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001454534266 none C[C@H]1Cc2cnccc2N1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 6, 6, 6, 6] 46 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 64) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1Cc2cnccc2N1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001454534266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454534266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001454534266 none C[C@H]1Cc2cnccc2N1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 3, 12, 12, 3, 3, 3, 3] 33 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454534266 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454534266 Building ZINC001454663489 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454663489 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/65 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c2ccccn2)cn1) `ZINC001454663489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454663489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663489 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 3, 3, 3, 12, 12, 22, 12, 28, 28, 28, 35, 35, 35, 35, 35, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 3, 22, 22, 66, 84, 35, 35, 35, 35, 5] 450 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: 355 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/66 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c2ccccn2)cn1) `ZINC001454663489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454663489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663489 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 11, 21, 11, 29, 29, 29, 35, 35, 35, 35, 35, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 21, 21, 63, 87, 35, 35, 35, 35, 5] 450 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: 343 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454663489 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489 Building ZINC001454663489 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454663489 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 65) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c2ccccn2)cn1) `ZINC001454663489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454663489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663489 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 3, 3, 3, 12, 12, 22, 12, 28, 28, 28, 35, 35, 35, 35, 35, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 3, 22, 22, 66, 84, 35, 35, 35, 35, 5] 450 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: 355 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 66) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c2ccccn2)cn1) `ZINC001454663489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454663489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663489 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 11, 21, 11, 29, 29, 29, 35, 35, 35, 35, 35, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 21, 21, 63, 87, 35, 35, 35, 35, 5] 450 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: 343 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454663489 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663489 Building ZINC001454663491 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454663491 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/67 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c2ccccn2)cn1) `ZINC001454663491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454663491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663491 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 22, 10, 28, 28, 28, 36, 36, 36, 36, 36, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 22, 22, 66, 84, 36, 36, 36, 36, 5] 450 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: 361 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/68 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c2ccccn2)cn1) `ZINC001454663491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454663491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663491 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 22, 10, 26, 26, 26, 35, 35, 35, 35, 35, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 22, 22, 66, 78, 35, 35, 35, 35, 6] 450 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: 361 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454663491 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491 Building ZINC001454663491 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454663491 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 67) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c2ccccn2)cn1) `ZINC001454663491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454663491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663491 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 22, 10, 28, 28, 28, 36, 36, 36, 36, 36, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 22, 22, 66, 84, 36, 36, 36, 36, 5] 450 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: 361 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 68) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/68: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c2ccccn2)cn1) `ZINC001454663491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454663491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663491 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 22, 10, 26, 26, 26, 35, 35, 35, 35, 35, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 22, 22, 66, 78, 35, 35, 35, 35, 6] 450 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: 361 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454663491 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663491 Building ZINC001454663493 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454663493 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/69 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c2ccccn2)cn1) `ZINC001454663493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454663493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663493 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 20, 10, 28, 28, 28, 40, 40, 40, 40, 40, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 20, 20, 60, 84, 40, 40, 40, 40, 5] 450 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: 347 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/70 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c2ccccn2)cn1) `ZINC001454663493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454663493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663493 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 21, 10, 24, 24, 24, 39, 39, 39, 39, 39, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 21, 21, 63, 72, 39, 39, 39, 39, 5] 450 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: 338 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454663493 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493 Building ZINC001454663493 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454663493 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 69) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/69: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c2ccccn2)cn1) `ZINC001454663493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454663493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663493 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 20, 10, 28, 28, 28, 40, 40, 40, 40, 40, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 20, 20, 60, 84, 40, 40, 40, 40, 5] 450 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: 347 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 70) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c2ccccn2)cn1) `ZINC001454663493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454663493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663493 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 21, 10, 24, 24, 24, 39, 39, 39, 39, 39, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 21, 21, 63, 72, 39, 39, 39, 39, 5] 450 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: 338 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454663493 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663493 Building ZINC001454663494 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454663494 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/71 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c2ccccn2)cn1) `ZINC001454663494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454663494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663494 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 19, 10, 24, 24, 24, 37, 37, 37, 37, 37, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 19, 19, 57, 72, 37, 37, 37, 37, 5] 450 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: 317 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/72 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c2ccccn2)cn1) `ZINC001454663494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454663494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663494 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 18, 10, 26, 26, 26, 42, 42, 42, 42, 42, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 18, 18, 54, 78, 42, 42, 42, 42, 5] 450 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: 327 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454663494 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494 Building ZINC001454663494 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454663494 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 71) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c2ccccn2)cn1) `ZINC001454663494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454663494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663494 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 19, 10, 24, 24, 24, 37, 37, 37, 37, 37, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 19, 19, 57, 72, 37, 37, 37, 37, 5] 450 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: 317 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 72) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/72: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c2ccccn2)cn1) `ZINC001454663494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454663494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454663494 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 18, 10, 26, 26, 26, 42, 42, 42, 42, 42, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 18, 18, 54, 78, 42, 42, 42, 42, 5] 450 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: 327 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454663494 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454663494 Building ZINC001454666373 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454666373 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/73 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1) `ZINC001454666373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454666373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001454666373 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 8, 8, 6, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 19, 20, 20, 19, 20, 20, 8, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 4, 19, 19, 20, 20, 20, 20, 20, 63, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/74 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1) `ZINC001454666373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454666373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001454666373 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 8, 8, 6, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 11, 11, 24, 25, 25, 24, 25, 25, 11, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 5, 24, 24, 25, 25, 25, 25, 25, 81, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454666373 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373 Building ZINC001454666373 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454666373 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 73) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/73: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1) `ZINC001454666373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454666373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001454666373 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 8, 8, 6, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 19, 20, 20, 19, 20, 20, 8, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 4, 19, 19, 20, 20, 20, 20, 20, 63, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 74) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1) `ZINC001454666373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454666373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001454666373 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 8, 8, 6, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 11, 11, 24, 25, 25, 24, 25, 25, 11, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 5, 24, 24, 25, 25, 25, 25, 25, 81, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454666373 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666373 Building ZINC001454666374 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454666374 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/75 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1) `ZINC001454666374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454666374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001454666374 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 8, 8, 6, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 9, 9, 21, 22, 22, 22, 22, 22, 9, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 5, 21, 21, 22, 22, 22, 22, 22, 63, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/76 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/76' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1) `ZINC001454666374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454666374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001454666374 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 8, 8, 6, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 20, 21, 21, 20, 21, 21, 8, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 4, 20, 20, 21, 21, 20, 21, 21, 66, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454666374 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374 Building ZINC001454666374 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454666374 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 75) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1) `ZINC001454666374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454666374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001454666374 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 8, 8, 6, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 9, 9, 21, 22, 22, 22, 22, 22, 9, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 5, 21, 21, 22, 22, 22, 22, 22, 63, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 76) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1) `ZINC001454666374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454666374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001454666374 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc(O)n[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 8, 8, 6, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 20, 21, 21, 20, 21, 21, 8, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 4, 20, 20, 21, 21, 20, 21, 21, 66, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454666374 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454666374 Building ZINC001454667795 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454667795 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/77 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1ccccn1) `ZINC001454667795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454667795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667795 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 18, 18, 32, 18, 35, 35, 35, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 5, 32, 32, 96, 105, 40, 40, 40, 40] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 428 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/78 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/78' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1ccccn1) `ZINC001454667795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454667795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667795 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 5, 20, 20, 36, 20, 37, 37, 37, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 5, 36, 36, 108, 111, 45, 45, 45, 45] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 472 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454667795 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795 Building ZINC001454667795 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454667795 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 77) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CO)[C@@H](O)c1ccccn1) `ZINC001454667795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454667795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667795 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 18, 18, 32, 18, 35, 35, 35, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 5, 32, 32, 96, 105, 40, 40, 40, 40] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 428 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 78) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CO)[C@@H](O)c1ccccn1) `ZINC001454667795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454667795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667795 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 5, 20, 20, 36, 20, 37, 37, 37, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 5, 36, 36, 108, 111, 45, 45, 45, 45] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 472 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454667795 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667795 Building ZINC001454667798 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454667798 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/79 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1ccccn1) `ZINC001454667798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454667798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667798 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 23, 23, 35, 23, 38, 38, 38, 46, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 3, 6, 35, 35, 105, 114, 46, 46, 46, 46] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 445 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/80 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1ccccn1) `ZINC001454667798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454667798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667798 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 18, 18, 33, 18, 36, 36, 36, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 5, 33, 33, 99, 108, 45, 45, 45, 45] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 451 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454667798 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798 Building ZINC001454667798 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454667798 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 79) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CO)[C@@H](O)c1ccccn1) `ZINC001454667798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454667798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667798 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 23, 23, 35, 23, 38, 38, 38, 46, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 3, 6, 35, 35, 105, 114, 46, 46, 46, 46] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 445 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 80) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CO)[C@@H](O)c1ccccn1) `ZINC001454667798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454667798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667798 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 18, 18, 33, 18, 36, 36, 36, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 5, 33, 33, 99, 108, 45, 45, 45, 45] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 451 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454667798 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667798 Building ZINC001454667802 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454667802 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/81 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1ccccn1) `ZINC001454667802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454667802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667802 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 5, 19, 19, 35, 19, 36, 36, 36, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 35, 35, 105, 108, 44, 44, 44, 44] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 463 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/82 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1ccccn1) `ZINC001454667802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454667802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667802 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 18, 18, 32, 18, 34, 34, 34, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 6, 32, 32, 96, 102, 40, 40, 40, 40] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 417 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454667802 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802 Building ZINC001454667802 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454667802 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 81) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CO)[C@H](O)c1ccccn1) `ZINC001454667802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454667802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667802 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 5, 19, 19, 35, 19, 36, 36, 36, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 35, 35, 105, 108, 44, 44, 44, 44] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 463 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 82) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CO)[C@H](O)c1ccccn1) `ZINC001454667802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454667802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667802 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 18, 18, 32, 18, 34, 34, 34, 40, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 6, 32, 32, 96, 102, 40, 40, 40, 40] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 417 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454667802 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667802 Building ZINC001454667806 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454667806 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/83 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1ccccn1) `ZINC001454667806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454667806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667806 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 18, 18, 33, 18, 36, 36, 36, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 5, 33, 33, 99, 108, 45, 45, 45, 45] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 451 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/84 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/84' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1ccccn1) `ZINC001454667806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454667806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667806 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 20, 20, 37, 20, 40, 40, 40, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 6, 37, 37, 111, 120, 47, 47, 47, 47] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 496 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454667806 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806 Building ZINC001454667806 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454667806 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 83) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CO)[C@H](O)c1ccccn1) `ZINC001454667806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454667806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667806 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 18, 18, 33, 18, 36, 36, 36, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 5, 33, 33, 99, 108, 45, 45, 45, 45] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 451 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 84) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CO)[C@H](O)c1ccccn1) `ZINC001454667806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454667806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454667806 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 20, 20, 37, 20, 40, 40, 40, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 6, 37, 37, 111, 120, 47, 47, 47, 47] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 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: 496 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454667806 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454667806 Building ZINC001454678287 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454678287 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/85 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1cccnc1) `ZINC001454678287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454678287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678287 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 17, 30, 17, 31, 31, 31, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 30, 30, 90, 93, 50, 50, 50, 50] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 415 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/86 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1cccnc1) `ZINC001454678287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454678287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678287 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 17, 32, 17, 34, 34, 34, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 32, 32, 96, 102, 50, 50, 50, 50] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 446 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454678287 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287 Building ZINC001454678287 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454678287 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 85) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1cccnc1) `ZINC001454678287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454678287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678287 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 17, 30, 17, 31, 31, 31, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 30, 30, 90, 93, 50, 50, 50, 50] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 415 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 86) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1cccnc1) `ZINC001454678287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454678287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678287 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 17, 32, 17, 34, 34, 34, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 32, 32, 96, 102, 50, 50, 50, 50] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 446 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454678287 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678287 Building ZINC001454678288 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454678288 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/87 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1cccnc1) `ZINC001454678288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454678288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678288 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 19, 19, 31, 19, 31, 31, 31, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 4, 31, 31, 93, 93, 49, 49, 49, 49] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 423 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/88 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1cccnc1) `ZINC001454678288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454678288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678288 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 14, 14, 30, 14, 28, 28, 28, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 30, 30, 90, 84, 50, 50, 50, 50] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 416 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454678288 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288 Building ZINC001454678288 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454678288 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 87) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1cccnc1) `ZINC001454678288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454678288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678288 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 19, 19, 31, 19, 31, 31, 31, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 4, 31, 31, 93, 93, 49, 49, 49, 49] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 423 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 88) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1cccnc1) `ZINC001454678288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454678288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678288 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 14, 14, 30, 14, 28, 28, 28, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 30, 30, 90, 84, 50, 50, 50, 50] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 416 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454678288 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678288 Building ZINC001454678289 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454678289 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/89 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1cccnc1) `ZINC001454678289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454678289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678289 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 13, 13, 29, 13, 28, 28, 28, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 29, 29, 87, 84, 50, 50, 50, 50] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 410 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/90 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1cccnc1) `ZINC001454678289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454678289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678289 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 19, 19, 31, 19, 31, 31, 31, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 4, 31, 31, 93, 93, 49, 49, 49, 49] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 423 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454678289 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289 Building ZINC001454678289 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454678289 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 89) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1cccnc1) `ZINC001454678289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454678289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678289 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 13, 13, 29, 13, 28, 28, 28, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 29, 29, 87, 84, 50, 50, 50, 50] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 410 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 90) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1cccnc1) `ZINC001454678289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454678289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678289 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)[C@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 19, 19, 31, 19, 31, 31, 31, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 4, 31, 31, 93, 93, 49, 49, 49, 49] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 423 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454678289 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678289 Building ZINC001454678290 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454678290 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/91 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1cccnc1) `ZINC001454678290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454678290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678290 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 17, 31, 17, 34, 34, 34, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 31, 31, 93, 102, 50, 50, 50, 50] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 440 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/92 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1cccnc1) `ZINC001454678290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454678290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678290 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 17, 30, 17, 31, 31, 31, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 30, 30, 90, 93, 50, 50, 50, 50] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 415 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454678290 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290 Building ZINC001454678290 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454678290 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 91) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1cccnc1) `ZINC001454678290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454678290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678290 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 17, 31, 17, 34, 34, 34, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 31, 31, 93, 102, 50, 50, 50, 50] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 440 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 92) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1cccnc1) `ZINC001454678290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454678290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001454678290 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)[C@H](O)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 7, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 17, 30, 17, 31, 31, 31, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 30, 30, 90, 93, 50, 50, 50, 50] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 415 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454678290 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454678290 Building ZINC001454768586 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454768586 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/93 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC(C)(C)CS(N)(=O)=O)cn1) `ZINC001454768586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454768586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454768586 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC(C)(C)CS(N)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 23, 23, 21, 33, 34, 34, 34, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 12, 12, 23, 23, 23, 23, 23, 23, 33, 33, 34, 34, 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]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/94 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC(C)(C)CS(N)(=O)=O)cn1) `ZINC001454768586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454768586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454768586 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC(C)(C)CS(N)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 23, 23, 21, 34, 35, 35, 35, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 12, 12, 23, 23, 23, 23, 23, 23, 34, 34, 35, 35, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454768586 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586 Building ZINC001454768586 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454768586 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 93) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC(C)(C)CS(N)(=O)=O)cn1) `ZINC001454768586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454768586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454768586 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC(C)(C)CS(N)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 23, 23, 21, 33, 34, 34, 34, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 12, 12, 23, 23, 23, 23, 23, 23, 33, 33, 34, 34, 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]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 94) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC(C)(C)CS(N)(=O)=O)cn1) `ZINC001454768586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454768586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001454768586 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC(C)(C)CS(N)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 23, 23, 21, 34, 35, 35, 35, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 12, 12, 23, 23, 23, 23, 23, 23, 34, 34, 35, 35, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001454768586 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001454768586 Building ZINC001455045225 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455045225 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/95 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C(N)=O)C1) `ZINC001455045225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455045225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455045225 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 1, 3, 3, 7, 7, 7, 32, 32, 7, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 4, 7, 7, 7, 32, 32, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/96 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C(N)=O)C1) `ZINC001455045225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455045225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455045225 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 1, 1, 1, 1, 5, 5, 9, 9, 9, 32, 32, 9, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 3, 9, 9, 9, 32, 32, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455045225 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225 Building ZINC001455045225 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455045225 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 95) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C(N)=O)C1) `ZINC001455045225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455045225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455045225 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 1, 3, 3, 7, 7, 7, 32, 32, 7, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 4, 7, 7, 7, 32, 32, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 96) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C(N)=O)C1) `ZINC001455045225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455045225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455045225 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 1, 1, 1, 1, 5, 5, 9, 9, 9, 32, 32, 9, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 3, 9, 9, 9, 32, 32, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455045225 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455045225 Building ZINC001455052799 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455052799 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/97 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O) `ZINC001455052799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455052799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455052799 none Cn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 81] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/98 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O) `ZINC001455052799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455052799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455052799 none Cn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 81] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455052799 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799 Building ZINC001455052799 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455052799 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 97) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O) `ZINC001455052799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455052799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455052799 none Cn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 81] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 98) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O) `ZINC001455052799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455052799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455052799 none Cn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 81] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455052799 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455052799 Building ZINC001455177717 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455177717 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/99 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OCc1ccccc1)[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001455177717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455177717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001455177717 none O=C(OCc1ccccc1)[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [22, 9, 22, 26, 49, 50, 50, 49, 50, 50, 6, 9, 9, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 49, 50, 50, 49, 50, 50, 27, 6, 6, 3, 2, 2, 4, 2, 2] 300 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]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/100 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OCc1ccccc1)[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001455177717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455177717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001455177717 none O=C(OCc1ccccc1)[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 24, 28, 48, 50, 50, 48, 50, 50, 6, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 48, 48, 50, 50, 48, 50, 50, 30, 6, 6, 2, 2, 2, 4, 2, 2] 300 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]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455177717 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717 Building ZINC001455177717 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455177717 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 99) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OCc1ccccc1)[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001455177717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455177717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001455177717 none O=C(OCc1ccccc1)[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [22, 9, 22, 26, 49, 50, 50, 49, 50, 50, 6, 9, 9, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 49, 50, 50, 49, 50, 50, 27, 6, 6, 3, 2, 2, 4, 2, 2] 300 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]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 100) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OCc1ccccc1)[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001455177717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455177717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001455177717 none O=C(OCc1ccccc1)[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 24, 28, 48, 50, 50, 48, 50, 50, 6, 10, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 48, 48, 50, 50, 48, 50, 50, 30, 6, 6, 2, 2, 2, 4, 2, 2] 300 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]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455177717 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455177717 Building ZINC001455244264 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455244264 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/101 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cn(C2CC2)c(=O)nc1O) `ZINC001455244264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455244264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455244264 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cn(C2CC2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 28, 46, 46, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 28, 46, 46, 46, 46, 46, 84] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/102 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cn(C2CC2)c(=O)nc1O) `ZINC001455244264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455244264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455244264 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cn(C2CC2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 30, 30, 30, 45, 45, 30, 30, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 30, 45, 45, 45, 45, 45, 90] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455244264 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264 Building ZINC001455244264 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455244264 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 101) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cn(C2CC2)c(=O)nc1O) `ZINC001455244264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455244264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455244264 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cn(C2CC2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 28, 46, 46, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 28, 46, 46, 46, 46, 46, 84] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 102) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cn(C2CC2)c(=O)nc1O) `ZINC001455244264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455244264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455244264 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cn(C2CC2)c(=O)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 5, 5, 1, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 30, 30, 30, 45, 45, 30, 30, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 30, 45, 45, 45, 45, 45, 90] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455244264 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455244264 Building ZINC001455263323 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455263323 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/103 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCCC[C@H]12) `ZINC001455263323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455263323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001455263323 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 14, 14, 14, 5, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 14, 14, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/104 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCCC[C@H]12) `ZINC001455263323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455263323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001455263323 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 15, 15, 5, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455263323 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323 Building ZINC001455263323 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455263323 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 103) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCCC[C@H]12) `ZINC001455263323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455263323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001455263323 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 14, 14, 14, 5, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 14, 14, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 104) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCCC[C@H]12) `ZINC001455263323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455263323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001455263323 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 15, 15, 5, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455263323 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455263323 Building ZINC001455293819 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455293819 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/105 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2nnc3c(=O)[nH]ccn23)c1) `ZINC001455293819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455293819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001455293819 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2nnc3c(=O)[nH]ccn23)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', '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, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 6, 6, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 2, 4, 4, 6, 6, 6, 20, 20, 29, 29, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/106 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N(C)Cc2nnc3c(=O)[nH]ccn23)c1) `ZINC001455293819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455293819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001455293819 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(C)Cc2nnc3c(=O)[nH]ccn23)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', '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, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 6, 6, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 19, 19, 29, 29, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455293819 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819 Building ZINC001455293819 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455293819 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 105) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2nnc3c(=O)[nH]ccn23)c1) `ZINC001455293819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455293819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001455293819 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2nnc3c(=O)[nH]ccn23)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', '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, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 6, 6, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 2, 4, 4, 6, 6, 6, 20, 20, 29, 29, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 106) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N(C)Cc2nnc3c(=O)[nH]ccn23)c1) `ZINC001455293819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455293819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001455293819 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(C)Cc2nnc3c(=O)[nH]ccn23)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', '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, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 6, 6, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 19, 19, 29, 29, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455293819 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455293819 Building ZINC001455320608 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455320608 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/107 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455320608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455320608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001455320608 none CNC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 18, 4, 10, 10, 23, 29, 29, 29, 29, 29, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 23, 23, 29, 29, 4, 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]) total number of confs: 144 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/108 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455320608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455320608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001455320608 none CNC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 20, 4, 10, 10, 21, 29, 29, 29, 29, 29, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 21, 21, 29, 29, 4, 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]) total number of confs: 142 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455320608 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608 Building ZINC001455320608 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455320608 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 107) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455320608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455320608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001455320608 none CNC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 18, 4, 10, 10, 23, 29, 29, 29, 29, 29, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 23, 23, 29, 29, 4, 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]) total number of confs: 144 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 108) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455320608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455320608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001455320608 none CNC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 20, 4, 10, 10, 21, 29, 29, 29, 29, 29, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 21, 21, 29, 29, 4, 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]) total number of confs: 142 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455320608 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455320608 Building ZINC001455333547 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455333547 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/109 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CO)CC1OCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001455333547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455333547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455333547 none O=C(N[C@H](CO)CC1OCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 10, 10, 21, 10, 25, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 21, 21, 63, 25, 25, 31, 31, 31, 31, 31, 4, 4, 4, 4] 150 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: 248 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/110 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CO)CC1OCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001455333547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455333547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455333547 none O=C(N[C@H](CO)CC1OCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 13, 23, 13, 27, 33, 33, 33, 33, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 23, 23, 69, 27, 27, 33, 33, 33, 33, 33, 4, 4, 4, 4] 150 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: 263 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455333547 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547 Building ZINC001455333547 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455333547 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 109) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](CO)CC1OCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001455333547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455333547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455333547 none O=C(N[C@H](CO)CC1OCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 10, 10, 21, 10, 25, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 21, 21, 63, 25, 25, 31, 31, 31, 31, 31, 4, 4, 4, 4] 150 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: 248 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 110) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](CO)CC1OCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001455333547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455333547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455333547 none O=C(N[C@H](CO)CC1OCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 13, 23, 13, 27, 33, 33, 33, 33, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 23, 23, 69, 27, 27, 33, 33, 33, 33, 33, 4, 4, 4, 4] 150 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: 263 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455333547 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333547 Building ZINC001455333554 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455333554 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/111 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)CC1OCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001455333554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455333554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455333554 none O=C(N[C@@H](CO)CC1OCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 13, 24, 13, 27, 32, 32, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 24, 24, 72, 27, 27, 32, 32, 32, 32, 32, 4, 4, 4, 4] 150 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: 265 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/112 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/112' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)CC1OCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001455333554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455333554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455333554 none O=C(N[C@@H](CO)CC1OCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 10, 10, 23, 10, 25, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 23, 23, 69, 25, 25, 31, 31, 31, 31, 31, 4, 4, 4, 4] 150 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: 264 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455333554 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554 Building ZINC001455333554 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455333554 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 111) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](CO)CC1OCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001455333554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455333554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455333554 none O=C(N[C@@H](CO)CC1OCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 13, 13, 24, 13, 27, 32, 32, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 24, 24, 72, 27, 27, 32, 32, 32, 32, 32, 4, 4, 4, 4] 150 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: 265 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 112) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](CO)CC1OCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001455333554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455333554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455333554 none O=C(N[C@@H](CO)CC1OCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 10, 10, 23, 10, 25, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 23, 23, 69, 25, 25, 31, 31, 31, 31, 31, 4, 4, 4, 4] 150 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: 264 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455333554 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455333554 Building ZINC001455341686 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455341686 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/113 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cnccc2NC1=O) `ZINC001455341686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455341686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455341686 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cnccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 39, 39, 39, 39, 39, 39] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/114 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cnccc2NC1=O) `ZINC001455341686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455341686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455341686 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cnccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 9, 9, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455341686 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686 Building ZINC001455341686 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455341686 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 113) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cnccc2NC1=O) `ZINC001455341686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455341686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455341686 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cnccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 39, 39, 39, 39, 39, 39] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 114) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cnccc2NC1=O) `ZINC001455341686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455341686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455341686 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cnccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 9, 9, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455341686 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341686 Building ZINC001455341690 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455341690 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/115 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1Cc2cnccc2NC1=O) `ZINC001455341690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455341690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455341690 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1Cc2cnccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 9, 9, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/116 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/116' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1Cc2cnccc2NC1=O) `ZINC001455341690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455341690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455341690 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1Cc2cnccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 39, 39, 39, 39, 39, 39] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455341690 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690 Building ZINC001455341690 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455341690 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 115) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1Cc2cnccc2NC1=O) `ZINC001455341690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455341690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455341690 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1Cc2cnccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 9, 9, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 116) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1Cc2cnccc2NC1=O) `ZINC001455341690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455341690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455341690 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1Cc2cnccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 39, 39, 39, 39, 39, 39] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455341690 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455341690 Building ZINC001455343723 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455343723 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/117 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O) `ZINC001455343723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455343723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455343723 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 39, 39, 39, 39, 39, 39] 45 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/118 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/118' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O) `ZINC001455343723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455343723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455343723 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 10, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455343723 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723 Building ZINC001455343723 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455343723 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 117) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O) `ZINC001455343723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455343723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455343723 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 39, 39, 39, 39, 39, 39] 45 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 118) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O) `ZINC001455343723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455343723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455343723 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 10, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455343723 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343723 Building ZINC001455343731 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455343731 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/119 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O) `ZINC001455343731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455343731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455343731 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 10, 10, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/120 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O) `ZINC001455343731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455343731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455343731 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 41, 41, 41, 41, 41, 41] 47 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455343731 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731 Building ZINC001455343731 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455343731 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 119) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O) `ZINC001455343731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455343731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455343731 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 10, 10, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 120) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O) `ZINC001455343731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455343731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455343731 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 41, 41, 41, 41, 41, 41] 47 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 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: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455343731 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455343731 Building ZINC001455354459 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455354459 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/121 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(Cc2nn[nH]n2)CC1) `ZINC001455354459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455354459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001455354459 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(Cc2nn[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', '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, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 6, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 3, 5, 10, 10, 10, 10, 29, 38, 38, 38, 38, 38, 10, 10, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 29, 29, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/122 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/122' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(Cc2nn[nH]n2)CC1) `ZINC001455354459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455354459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001455354459 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(Cc2nn[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', '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, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 6, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 5, 10, 10, 10, 10, 28, 38, 38, 38, 38, 38, 10, 10, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 28, 28, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455354459 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459 Building ZINC001455354459 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455354459 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 121) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCC(Cc2nn[nH]n2)CC1) `ZINC001455354459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455354459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001455354459 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(Cc2nn[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', '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, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 6, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 3, 5, 10, 10, 10, 10, 29, 38, 38, 38, 38, 38, 10, 10, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 29, 29, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 122) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N1CCC(Cc2nn[nH]n2)CC1) `ZINC001455354459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455354459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001455354459 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(Cc2nn[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', '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, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 6, 8, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 5, 10, 10, 10, 10, 28, 38, 38, 38, 38, 38, 10, 10, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 28, 28, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455354459 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455354459 Building ZINC001455356502 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455356502 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/123 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(Cc3nn[nH]n3)CC2)cn1) `ZINC001455356502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455356502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001455356502 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(Cc3nn[nH]n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 6, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 15, 28, 28, 28, 28, 28, 5, 5, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 5, 5, 5, 5, 5, 15, 15, 5, 5, 5, 5, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/124 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(Cc3nn[nH]n3)CC2)cn1) `ZINC001455356502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455356502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001455356502 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(Cc3nn[nH]n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 6, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 14, 30, 30, 30, 30, 30, 4, 4, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 4, 4, 4, 4, 4, 14, 14, 4, 4, 4, 4, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455356502 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502 Building ZINC001455356502 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455356502 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 123) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(Cc3nn[nH]n3)CC2)cn1) `ZINC001455356502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455356502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001455356502 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(Cc3nn[nH]n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 6, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 15, 28, 28, 28, 28, 28, 5, 5, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 5, 5, 5, 5, 5, 15, 15, 5, 5, 5, 5, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 124) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(Cc3nn[nH]n3)CC2)cn1) `ZINC001455356502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455356502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001455356502 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(Cc3nn[nH]n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 8, 8, 6, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 14, 30, 30, 30, 30, 30, 4, 4, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 4, 4, 4, 4, 4, 14, 14, 4, 4, 4, 4, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455356502 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455356502 Building ZINC001455369925 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455369925 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/125 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 16, 16, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 16, 16, 16, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/126 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 15, 15, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 15, 15, 15, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/127 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/127' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 16, 16, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 16, 16, 16, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/128 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/128' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 15, 15, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 15, 15, 15, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455369925 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 Building ZINC001455369925 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455369925 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 125) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 16, 16, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 16, 16, 16, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 126) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 15, 15, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 15, 15, 15, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 127) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 16, 16, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 16, 16, 16, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 128) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 15, 15, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 15, 15, 15, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455369925 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 Building ZINC001455369925 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455369925 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 125) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 16, 16, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 16, 16, 16, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 126) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 15, 15, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 15, 15, 15, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 127) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 16, 16, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 16, 16, 16, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 128) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 15, 15, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 15, 15, 15, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455369925 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 Building ZINC001455369925 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455369925 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 125) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 16, 16, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 16, 16, 16, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 126) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 15, 15, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 15, 15, 15, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 127) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 16, 16, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 16, 16, 16, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 128) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1) `ZINC001455369925.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455369925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001455369925 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCN(C)CCS(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 12, 15, 15, 18, 18, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 2, 10, 10, 12, 12, 15, 15, 15, 18, 18, 18, 18, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455369925 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455369925 Building ZINC001455694347 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455694347 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/129 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)nc1) `ZINC001455694347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455694347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001455694347 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)nc1 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', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 5, 11, 11, 8, 1, 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, 3, 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: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 46, 46, 46, 46, 50, 50, 50, 46, 46, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 46, 46, 50, 50, 50, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/130 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/130' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)nc1) `ZINC001455694347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455694347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001455694347 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)nc1 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', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 5, 11, 11, 8, 1, 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, 3, 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: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 46, 46, 46, 46, 50, 50, 50, 46, 46, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 46, 46, 50, 50, 50, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455694347 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347 Building ZINC001455694347 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455694347 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 129) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)nc1) `ZINC001455694347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455694347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001455694347 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)nc1 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', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 5, 11, 11, 8, 1, 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, 3, 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: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 46, 46, 46, 46, 50, 50, 50, 46, 46, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 46, 46, 50, 50, 50, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 130) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)nc1) `ZINC001455694347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455694347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001455694347 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)nc1 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', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 5, 11, 11, 8, 1, 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, 3, 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: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 46, 46, 46, 46, 50, 50, 50, 46, 46, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 46, 46, 50, 50, 50, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455694347 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455694347 Building ZINC001455813586 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455813586 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/131 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1CCCC2) `ZINC001455813586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455813586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001455813586 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 18, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 5, 5, 2, 2, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/132 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/132' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1CCCC2) `ZINC001455813586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455813586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001455813586 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 16, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 3, 2, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455813586 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586 Building ZINC001455813586 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455813586 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 131) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1CCCC2) `ZINC001455813586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455813586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001455813586 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 18, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 5, 5, 2, 2, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 132) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1CCCC2) `ZINC001455813586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455813586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001455813586 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 16, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 3, 2, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455813586 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813586 Building ZINC001455813602 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455813602 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/133 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@]12C[C@@H]1CCCC2) `ZINC001455813602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455813602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 19 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001455813602 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@]12C[C@@H]1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 16, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 3, 2, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/134 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/134' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@]12C[C@@H]1CCCC2) `ZINC001455813602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455813602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 19 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001455813602 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@]12C[C@@H]1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 18, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 5, 5, 2, 2, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455813602 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602 Building ZINC001455813602 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455813602 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 133) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@]12C[C@@H]1CCCC2) `ZINC001455813602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455813602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' Warning: atom stereo specified for planar atom 19 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001455813602 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@]12C[C@@H]1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 16, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 3, 2, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 134) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/134: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@]12C[C@@H]1CCCC2) `ZINC001455813602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455813602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' Warning: atom stereo specified for planar atom 19 warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001455813602 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@]12C[C@@H]1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 18, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 5, 5, 2, 2, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001455813602 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001455813602 Building ZINC001456056231 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456056231 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/135 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](CO)[C@H]1CO)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001456056231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456056231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001456056231 none O=C(N1CCC[C@@H](CO)[C@H]1CO)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 8, 11, 11, 11, 11, 11, 11, 18, 11, 11, 11, 20, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 11, 11, 11, 11, 11, 11, 18, 18, 54, 20, 20, 60, 6, 10, 10, 9, 10, 10, 6] 450 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 255 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/136 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/136' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](CO)[C@H]1CO)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001456056231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456056231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001456056231 none O=C(N1CCC[C@@H](CO)[C@H]1CO)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 9, 11, 11, 11, 11, 11, 11, 19, 11, 11, 11, 21, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 11, 11, 11, 11, 11, 11, 19, 19, 57, 21, 21, 63, 6, 13, 13, 6, 13, 13, 6] 450 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 277 number of broken/clashed sets: 166 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456056231 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231 Building ZINC001456056231 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456056231 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 135) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](CO)[C@H]1CO)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001456056231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456056231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001456056231 none O=C(N1CCC[C@@H](CO)[C@H]1CO)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 8, 11, 11, 11, 11, 11, 11, 18, 11, 11, 11, 20, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 11, 11, 11, 11, 11, 11, 18, 18, 54, 20, 20, 60, 6, 10, 10, 9, 10, 10, 6] 450 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 255 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 136) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](CO)[C@H]1CO)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001456056231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456056231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001456056231 none O=C(N1CCC[C@@H](CO)[C@H]1CO)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 9, 11, 11, 11, 11, 11, 11, 19, 11, 11, 11, 21, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 11, 11, 11, 11, 11, 11, 19, 19, 57, 21, 21, 63, 6, 13, 13, 6, 13, 13, 6] 450 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 277 number of broken/clashed sets: 166 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456056231 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456056231 Building ZINC001456154149 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456154149 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/137 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(O)nc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 46, 46, 21, 21, 21, 21, 6, 21, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 21, 21, 46, 46, 46, 46, 46, 92, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 100 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/138 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(O)nc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 45, 45, 45, 45, 22, 22, 22, 22, 6, 22, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 22, 22, 45, 45, 45, 45, 45, 90, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22] 100 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/139 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/139' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(O)nc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 44, 44, 44, 22, 22, 22, 22, 6, 22, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 44, 44, 44, 44, 44, 88, 22, 22, 22, 22, 3, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22] 100 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/140 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/140' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(O)nc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 44, 44, 44, 22, 22, 22, 22, 6, 22, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 44, 44, 44, 44, 44, 88, 22, 22, 22, 22, 3, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22] 100 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456154149 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 Building ZINC001456154149 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456154149 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 137) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/137: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 46, 46, 21, 21, 21, 21, 6, 21, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 21, 21, 46, 46, 46, 46, 46, 92, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 100 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 138) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 45, 45, 45, 45, 22, 22, 22, 22, 6, 22, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 22, 22, 45, 45, 45, 45, 45, 90, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22] 100 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 139) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 44, 44, 44, 22, 22, 22, 22, 6, 22, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 44, 44, 44, 44, 44, 88, 22, 22, 22, 22, 3, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22] 100 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 140) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 44, 44, 44, 22, 22, 22, 22, 6, 22, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 44, 44, 44, 44, 44, 88, 22, 22, 22, 22, 3, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22] 100 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456154149 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 Building ZINC001456154149 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456154149 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 137) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/137: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 46, 46, 21, 21, 21, 21, 6, 21, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 21, 21, 46, 46, 46, 46, 46, 92, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 100 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 138) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 45, 45, 45, 45, 22, 22, 22, 22, 6, 22, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 22, 22, 45, 45, 45, 45, 45, 90, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22] 100 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 139) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 44, 44, 44, 22, 22, 22, 22, 6, 22, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 44, 44, 44, 44, 44, 88, 22, 22, 22, 22, 3, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22] 100 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 140) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 44, 44, 44, 22, 22, 22, 22, 6, 22, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 44, 44, 44, 44, 44, 88, 22, 22, 22, 22, 3, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22] 100 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456154149 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 Building ZINC001456154149 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456154149 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 137) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/137: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 46, 46, 21, 21, 21, 21, 6, 21, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 21, 21, 46, 46, 46, 46, 46, 92, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 100 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 138) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 45, 45, 45, 45, 22, 22, 22, 22, 6, 22, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 22, 22, 45, 45, 45, 45, 45, 90, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22] 100 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 139) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 44, 44, 44, 22, 22, 22, 22, 6, 22, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 44, 44, 44, 44, 44, 88, 22, 22, 22, 22, 3, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22] 100 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 140) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1) `ZINC001456154149.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456154149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001456154149 none Cc1cc(O)nc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3cccn3C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 8, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 44, 44, 44, 22, 22, 22, 22, 6, 22, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 44, 44, 44, 44, 44, 88, 22, 22, 22, 22, 3, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22] 100 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456154149 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456154149 Building ZINC001456237573 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456237573 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/141 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(O)nc(CCN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)nc1O) `ZINC001456237573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456237573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001456237573 none Cc1c(O)nc(CCN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 400 conformations in input total number of sets (complete confs): 400 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 50, 50, 50, 21, 19, 8, 4, 8, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 100, 21, 21, 19, 19, 8, 8, 8, 2, 2, 4, 2, 2, 100] 400 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 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: 501 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/142 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(O)nc(CCN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)nc1O) `ZINC001456237573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456237573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001456237573 none Cc1c(O)nc(CCN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 400 conformations in input total number of sets (complete confs): 400 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 50, 50, 50, 20, 18, 7, 4, 7, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 100, 20, 20, 18, 18, 7, 7, 7, 2, 2, 4, 2, 2, 100] 400 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 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: 510 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456237573 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573 Building ZINC001456237573 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456237573 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 141) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(O)nc(CCN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)nc1O) `ZINC001456237573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456237573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001456237573 none Cc1c(O)nc(CCN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 400 conformations in input total number of sets (complete confs): 400 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 50, 50, 50, 21, 19, 8, 4, 8, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 100, 21, 21, 19, 19, 8, 8, 8, 2, 2, 4, 2, 2, 100] 400 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 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: 501 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 142) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(O)nc(CCN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)nc1O) `ZINC001456237573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456237573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001456237573 none Cc1c(O)nc(CCN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 400 conformations in input total number of sets (complete confs): 400 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 50, 50, 50, 20, 18, 7, 4, 7, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 100, 20, 20, 18, 18, 7, 7, 7, 2, 2, 4, 2, 2, 100] 400 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 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: 510 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456237573 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456237573 Building ZINC001456309477 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456309477 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/143 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc(CS(C)(=O)=O)n[nH]2)cc1) `ZINC001456309477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456309477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001456309477 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc(CS(C)(=O)=O)n[nH]2)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', 'N.2', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'H', '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, 1, 8, 1, 5, 14, 5, 11, 11, 8, 8, 6, 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, 7, 7, 7, 3, 3, 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: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 14, 14, 14, 35, 50, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 35, 35, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/144 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc(CS(C)(=O)=O)n[nH]2)cc1) `ZINC001456309477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456309477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001456309477 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc(CS(C)(=O)=O)n[nH]2)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', 'N.2', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'H', '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, 1, 8, 1, 5, 14, 5, 11, 11, 8, 8, 6, 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, 7, 7, 7, 3, 3, 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: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 14, 14, 14, 35, 50, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 35, 35, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456309477 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477 Building ZINC001456309477 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456309477 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 143) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/143: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2nc(CS(C)(=O)=O)n[nH]2)cc1) `ZINC001456309477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456309477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001456309477 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc(CS(C)(=O)=O)n[nH]2)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', 'N.2', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'H', '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, 1, 8, 1, 5, 14, 5, 11, 11, 8, 8, 6, 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, 7, 7, 7, 3, 3, 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: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 14, 14, 14, 35, 50, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 35, 35, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 144) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2nc(CS(C)(=O)=O)n[nH]2)cc1) `ZINC001456309477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456309477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001456309477 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc(CS(C)(=O)=O)n[nH]2)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', 'N.2', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'H', '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, 1, 8, 1, 5, 14, 5, 11, 11, 8, 8, 6, 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, 7, 7, 7, 3, 3, 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: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 14, 14, 14, 35, 50, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 35, 35, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456309477 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456309477 Building ZINC001456470650 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456470650 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/145 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)C1CC1) `ZINC001456470650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456470650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001456470650 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 12, 24, 24, 1, 1, 1, 1, 4, 4, 1, 2, 9, 9, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 22, 23, 24, 25, 28] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/146 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/146' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)C1CC1) `ZINC001456470650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456470650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001456470650 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 14, 12, 27, 27, 1, 1, 1, 1, 4, 4, 1, 2, 9, 9, 15, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 22, 23, 24, 25, 28] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456470650 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650 Building ZINC001456470650 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456470650 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 145) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)C1CC1) `ZINC001456470650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456470650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001456470650 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 12, 24, 24, 1, 1, 1, 1, 4, 4, 1, 2, 9, 9, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 22, 23, 24, 25, 28] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 146) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)C1CC1) `ZINC001456470650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456470650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001456470650 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 14, 12, 27, 27, 1, 1, 1, 1, 4, 4, 1, 2, 9, 9, 15, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 22, 23, 24, 25, 28] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456470650 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456470650 Building ZINC001456594729 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456594729 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/147 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456594729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456594729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001456594729 none CS(=O)(=O)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 24, 38, 38, 19, 14, 19, 19, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 38, 38, 38, 24, 24, 57, 14, 14, 5, 7, 7] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 246 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/148 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/148' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456594729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456594729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001456594729 none CS(=O)(=O)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 24, 36, 36, 19, 14, 19, 19, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 36, 36, 36, 24, 24, 57, 14, 14, 4, 7, 7] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 232 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456594729 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729 Building ZINC001456594729 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456594729 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 147) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456594729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456594729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001456594729 none CS(=O)(=O)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 24, 38, 38, 19, 14, 19, 19, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 38, 38, 38, 24, 24, 57, 14, 14, 5, 7, 7] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 246 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 148) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456594729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456594729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001456594729 none CS(=O)(=O)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 24, 36, 36, 19, 14, 19, 19, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 36, 36, 36, 24, 24, 57, 14, 14, 4, 7, 7] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 232 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456594729 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594729 Building ZINC001456594733 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456594733 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/149 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456594733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456594733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001456594733 none CS(=O)(=O)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 24, 37, 37, 19, 14, 19, 19, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 37, 37, 37, 24, 24, 57, 14, 14, 4, 7, 7] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 238 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/150 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456594733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456594733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001456594733 none CS(=O)(=O)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 26, 39, 39, 20, 14, 20, 20, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 39, 39, 39, 26, 26, 60, 14, 14, 5, 7, 7] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 255 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456594733 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733 Building ZINC001456594733 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456594733 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 149) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456594733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456594733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001456594733 none CS(=O)(=O)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 24, 37, 37, 19, 14, 19, 19, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 37, 37, 37, 24, 24, 57, 14, 14, 4, 7, 7] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 238 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 150) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456594733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456594733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001456594733 none CS(=O)(=O)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 26, 39, 39, 20, 14, 20, 20, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 39, 39, 39, 26, 26, 60, 14, 14, 5, 7, 7] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 255 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456594733 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456594733 Building ZINC001456677792 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456677792 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/151 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CON(C(=O)OC(C)(C)C)C2)cn1) `ZINC001456677792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456677792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001456677792 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CON(C(=O)OC(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 11, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/152 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/152' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CON(C(=O)OC(C)(C)C)C2)cn1) `ZINC001456677792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456677792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001456677792 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CON(C(=O)OC(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 5, 5, 13, 13, 13, 13, 13, 5, 2, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/83982/xcb-8058097.54/working/building/ZINC001456677792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456677792 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792 Building ZINC001456677792 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456677792 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 151) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CON(C(=O)OC(C)(C)C)C2)cn1) `ZINC001456677792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456677792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001456677792 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CON(C(=O)OC(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 11, 5, 5, 12, 12, 12, 12, 12, 5, 2, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 152) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CON(C(=O)OC(C)(C)C)C2)cn1) `ZINC001456677792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456677792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001456677792 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CON(C(=O)OC(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 11, 5, 5, 13, 13, 13, 13, 13, 5, 2, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/83982/xcb-8058097.54/working/building/ZINC001456677792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456677792 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456677792 Building ZINC001456779869 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456779869 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/153 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(C1)CC(=O)Nc1nccn12)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001456779869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456779869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001456779869 none O=C(N1CC2(C1)CC(=O)Nc1nccn12)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/154 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(C1)CC(=O)Nc1nccn12)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001456779869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456779869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001456779869 none O=C(N1CC2(C1)CC(=O)Nc1nccn12)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/83982/xcb-8058097.54/working/building/ZINC001456779869 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456779869 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869 Building ZINC001456779869 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456779869 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 153) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(C1)CC(=O)Nc1nccn12)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001456779869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456779869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001456779869 none O=C(N1CC2(C1)CC(=O)Nc1nccn12)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 154) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(C1)CC(=O)Nc1nccn12)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001456779869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456779869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001456779869 none O=C(N1CC2(C1)CC(=O)Nc1nccn12)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/83982/xcb-8058097.54/working/building/ZINC001456779869 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456779869 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456779869 Building ZINC001456991175 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456991175 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/155 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001456991175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456991175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001456991175 none CCCCC1(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 10, 6, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 6, 6, 16, 16, 16, 16, 16, 13, 13, 10, 10, 4, 4, 13, 13, 4, 4, 4, 4, 6, 6, 6, 6] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/156 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001456991175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456991175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001456991175 none CCCCC1(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 13, 8, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 8, 8, 18, 18, 18, 18, 18, 16, 16, 13, 13, 4, 4, 11, 11, 4, 4, 4, 4, 8, 8, 8, 8] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456991175 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175 Building ZINC001456991175 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456991175 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 155) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/155: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001456991175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456991175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001456991175 none CCCCC1(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 10, 6, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 6, 6, 16, 16, 16, 16, 16, 13, 13, 10, 10, 4, 4, 13, 13, 4, 4, 4, 4, 6, 6, 6, 6] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 156) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1) `ZINC001456991175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456991175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001456991175 none CCCCC1(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 13, 8, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 8, 8, 18, 18, 18, 18, 18, 16, 16, 13, 13, 4, 4, 11, 11, 4, 4, 4, 4, 8, 8, 8, 8] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001456991175 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001456991175 Building ZINC001457004789 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457004789 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/157 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@@H]21) `ZINC001457004789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457004789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004789 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 16, 16, 16, 6, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 16, 16, 6, 4, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/158 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@@H]21) `ZINC001457004789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457004789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004789 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 18, 18, 5, 4, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457004789 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789 Building ZINC001457004789 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457004789 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 157) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@@H]21) `ZINC001457004789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457004789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004789 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 16, 16, 16, 6, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 16, 16, 6, 4, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 158) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@@H]21) `ZINC001457004789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457004789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004789 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 18, 18, 5, 4, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457004789 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004789 Building ZINC001457004790 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457004790 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/159 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@H]21) `ZINC001457004790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457004790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004790 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 3, 3, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 15, 15, 5, 3, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/160 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/160' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@H]21) `ZINC001457004790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457004790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004790 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 15, 15, 5, 3, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457004790 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790 Building ZINC001457004790 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457004790 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 159) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@H]21) `ZINC001457004790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457004790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004790 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 3, 3, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 15, 15, 5, 3, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 160) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@H]21) `ZINC001457004790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457004790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004790 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CCC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 15, 15, 15, 5, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 15, 15, 5, 3, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457004790 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004790 Building ZINC001457004792 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457004792 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/161 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@H]12) `ZINC001457004792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457004792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004792 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 14, 14, 14, 5, 1, 1, 1, 1, 3, 3, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 14, 14, 5, 3, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/162 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/162' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@H]12) `ZINC001457004792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457004792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004792 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 1, 3, 3, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 13, 13, 4, 3, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457004792 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792 Building ZINC001457004792 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457004792 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 161) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@H]12) `ZINC001457004792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457004792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004792 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 14, 14, 14, 5, 1, 1, 1, 1, 3, 3, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 14, 14, 5, 3, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 162) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@H]12) `ZINC001457004792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457004792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004792 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 1, 3, 3, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 13, 13, 4, 3, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457004792 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004792 Building ZINC001457004794 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457004794 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/163 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@@H]12) `ZINC001457004794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457004794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004794 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 20, 20, 20, 6, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 20, 20, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/164 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@@H]12) `ZINC001457004794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457004794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004794 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 18, 18, 18, 6, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 18, 18, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457004794 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794 Building ZINC001457004794 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457004794 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 163) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@@H]12) `ZINC001457004794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457004794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004794 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 20, 20, 20, 6, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 20, 20, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 164) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@@H]12) `ZINC001457004794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457004794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001457004794 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@@H]2CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 18, 18, 18, 6, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 18, 18, 6, 3, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457004794 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457004794 Building ZINC001457133482 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457133482 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/165 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CO)Cn2cnc3ccccc32)cn1) `ZINC001457133482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457133482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001457133482 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CO)Cn2cnc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 8, 8, 17, 8, 21, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 4, 8, 8, 8, 17, 17, 51, 21, 21, 29, 29, 29, 29, 29, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 209 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/166 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CO)Cn2cnc3ccccc32)cn1) `ZINC001457133482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457133482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001457133482 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CO)Cn2cnc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 7, 7, 16, 7, 20, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 3, 7, 7, 7, 16, 16, 48, 20, 20, 31, 31, 31, 31, 31, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 196 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457133482 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482 Building ZINC001457133482 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457133482 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 165) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CO)Cn2cnc3ccccc32)cn1) `ZINC001457133482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457133482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001457133482 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@](C)(CO)Cn2cnc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 8, 8, 17, 8, 21, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 4, 8, 8, 8, 17, 17, 51, 21, 21, 29, 29, 29, 29, 29, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 209 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 166) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CO)Cn2cnc3ccccc32)cn1) `ZINC001457133482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457133482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001457133482 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@](C)(CO)Cn2cnc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 7, 7, 16, 7, 20, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 3, 7, 7, 7, 16, 16, 48, 20, 20, 31, 31, 31, 31, 31, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 196 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457133482 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133482 Building ZINC001457133489 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457133489 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/167 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CO)Cn2cnc3ccccc32)cn1) `ZINC001457133489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457133489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001457133489 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CO)Cn2cnc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 7, 7, 16, 7, 20, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 3, 7, 7, 7, 16, 16, 48, 20, 20, 31, 31, 31, 31, 31, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 196 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/168 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CO)Cn2cnc3ccccc32)cn1) `ZINC001457133489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457133489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001457133489 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CO)Cn2cnc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 8, 8, 17, 8, 21, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 4, 8, 8, 8, 17, 17, 51, 21, 21, 29, 29, 29, 29, 29, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 209 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457133489 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489 Building ZINC001457133489 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457133489 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 167) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CO)Cn2cnc3ccccc32)cn1) `ZINC001457133489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457133489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001457133489 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@](C)(CO)Cn2cnc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 7, 7, 16, 7, 20, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 3, 7, 7, 7, 16, 16, 48, 20, 20, 31, 31, 31, 31, 31, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 196 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 168) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CO)Cn2cnc3ccccc32)cn1) `ZINC001457133489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457133489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001457133489 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](C)(CO)Cn2cnc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 8, 8, 17, 8, 21, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 4, 8, 8, 8, 17, 17, 51, 21, 21, 29, 29, 29, 29, 29, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 209 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457133489 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457133489 Building ZINC001457152113 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457152113 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/169 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(C2(O)CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)CCC1) `ZINC001457152113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457152113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001457152113 none COC(=O)C1(C2(O)CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 18, 29, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 18, 18, 18, 29, 29, 29, 21, 7, 7, 7, 7, 4, 4, 4, 4, 4, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 111 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/170 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(C2(O)CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)CCC1) `ZINC001457152113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457152113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001457152113 none COC(=O)C1(C2(O)CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 17, 29, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 29, 29, 29, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457152113 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113 Building ZINC001457152113 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457152113 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 169) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C1(C2(O)CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)CCC1) `ZINC001457152113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457152113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001457152113 none COC(=O)C1(C2(O)CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 18, 29, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 18, 18, 18, 29, 29, 29, 21, 7, 7, 7, 7, 4, 4, 4, 4, 4, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 111 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 170) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)C1(C2(O)CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)CCC1) `ZINC001457152113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457152113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001457152113 none COC(=O)C1(C2(O)CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 17, 29, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 29, 29, 29, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457152113 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457152113 Building ZINC001546088133 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546088133 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/171 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(O)cc1F) `ZINC001546088133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546088133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001546088133 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(O)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 3, 3, 3, 11, 11, 9, 11, 11, 11, 11, 5, 5, 5, 5, 19, 19, 5, 3, 11, 11, 22, 11] 100 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/172 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(O)cc1F) `ZINC001546088133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546088133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001546088133 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(O)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 3, 3, 3, 11, 11, 6, 11, 11, 11, 11, 5, 5, 5, 5, 19, 19, 5, 3, 11, 11, 22, 11] 100 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001546088133 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133 Building ZINC001546088133 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546088133 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 171) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(O)cc1F) `ZINC001546088133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546088133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001546088133 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(O)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 3, 3, 3, 11, 11, 9, 11, 11, 11, 11, 5, 5, 5, 5, 19, 19, 5, 3, 11, 11, 22, 11] 100 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 172) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(O)cc1F) `ZINC001546088133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546088133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001546088133 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(O)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 3, 3, 3, 11, 11, 6, 11, 11, 11, 11, 5, 5, 5, 5, 19, 19, 5, 3, 11, 11, 22, 11] 100 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001546088133 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001546088133 Building ZINC001457180028 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457180028 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/173 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1) `ZINC001457180028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 11, 24, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 19, 11, 24, 24, 24, 3, 5, 5, 5, 5, 11, 11, 19, 19, 57, 11, 11] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/174 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1) `ZINC001457180028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 11, 24, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 19, 11, 24, 24, 24, 3, 5, 5, 5, 5, 11, 11, 19, 19, 57, 11, 11] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/175 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/175' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1) `ZINC001457180028.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 12, 25, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 20, 12, 25, 25, 25, 3, 5, 5, 5, 5, 12, 12, 20, 20, 60, 12, 12] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/176 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/176' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1) `ZINC001457180028.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 12, 27, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 19, 12, 27, 27, 27, 3, 4, 4, 4, 4, 12, 12, 19, 19, 57, 12, 12] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457180028 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 Building ZINC001457180028 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457180028 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 173) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1) `ZINC001457180028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 11, 24, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 19, 11, 24, 24, 24, 3, 5, 5, 5, 5, 11, 11, 19, 19, 57, 11, 11] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 174) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1) `ZINC001457180028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 11, 24, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 19, 11, 24, 24, 24, 3, 5, 5, 5, 5, 11, 11, 19, 19, 57, 11, 11] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 175) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1) `ZINC001457180028.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 12, 25, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 20, 12, 25, 25, 25, 3, 5, 5, 5, 5, 12, 12, 20, 20, 60, 12, 12] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 176) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1) `ZINC001457180028.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 12, 27, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 19, 12, 27, 27, 27, 3, 4, 4, 4, 4, 12, 12, 19, 19, 57, 12, 12] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457180028 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 Building ZINC001457180028 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457180028 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 173) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1) `ZINC001457180028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 11, 24, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 19, 11, 24, 24, 24, 3, 5, 5, 5, 5, 11, 11, 19, 19, 57, 11, 11] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 174) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1) `ZINC001457180028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 11, 24, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 19, 11, 24, 24, 24, 3, 5, 5, 5, 5, 11, 11, 19, 19, 57, 11, 11] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 175) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1) `ZINC001457180028.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 12, 25, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 20, 12, 25, 25, 25, 3, 5, 5, 5, 5, 12, 12, 20, 20, 60, 12, 12] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 176) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1) `ZINC001457180028.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 12, 27, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 19, 12, 27, 27, 27, 3, 4, 4, 4, 4, 12, 12, 19, 19, 57, 12, 12] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457180028 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 Building ZINC001457180028 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457180028 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 173) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1) `ZINC001457180028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 11, 24, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 19, 11, 24, 24, 24, 3, 5, 5, 5, 5, 11, 11, 19, 19, 57, 11, 11] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 174) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1) `ZINC001457180028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 11, 24, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 19, 11, 24, 24, 24, 3, 5, 5, 5, 5, 11, 11, 19, 19, 57, 11, 11] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 175) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1) `ZINC001457180028.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 12, 25, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 20, 12, 25, 25, 25, 3, 5, 5, 5, 5, 12, 12, 20, 20, 60, 12, 12] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 176) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1) `ZINC001457180028.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457180028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457180028 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 12, 27, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 19, 12, 27, 27, 27, 3, 4, 4, 4, 4, 12, 12, 19, 19, 57, 12, 12] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457180028 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457180028 Building ZINC001457184039 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457184039 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/177 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2cn(C)nn2)C1) `ZINC001457184039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457184039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457184039 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 6, 7, 15, 15, 15, 15, 15, 15, 40, 40, 40, 40, 40, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 40, 40, 40, 40, 15, 15] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/178 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2cn(C)nn2)C1) `ZINC001457184039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457184039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457184039 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 7, 10, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 15, 15] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457184039 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039 Building ZINC001457184039 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457184039 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 177) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2cn(C)nn2)C1) `ZINC001457184039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457184039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457184039 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 6, 7, 15, 15, 15, 15, 15, 15, 40, 40, 40, 40, 40, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 40, 40, 40, 40, 15, 15] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 178) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2cn(C)nn2)C1) `ZINC001457184039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457184039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457184039 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 7, 10, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 15, 15] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457184039 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184039 Building ZINC001457184056 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457184056 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/179 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2cn(C)nn2)C1) `ZINC001457184056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457184056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457184056 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 10, 15, 15, 15, 15, 15, 15, 33, 33, 33, 33, 33, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 33, 33, 33, 33, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 58 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/180 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/180' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2cn(C)nn2)C1) `ZINC001457184056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457184056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457184056 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 8, 15, 15, 15, 15, 15, 15, 41, 41, 41, 41, 41, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 41, 41, 41, 41, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457184056 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056 Building ZINC001457184056 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457184056 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 179) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2cn(C)nn2)C1) `ZINC001457184056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457184056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457184056 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 10, 15, 15, 15, 15, 15, 15, 33, 33, 33, 33, 33, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 33, 33, 33, 33, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 58 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 180) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2cn(C)nn2)C1) `ZINC001457184056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457184056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457184056 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](c2cn(C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 8, 15, 15, 15, 15, 15, 15, 41, 41, 41, 41, 41, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 41, 41, 41, 41, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457184056 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457184056 Building ZINC001457320028 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457320028 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/181 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001457320028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457320028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001457320028 none CN1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 10, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 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, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 22, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 4, 6, 6, 6, 6, 25, 25, 25, 25] 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: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/182 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001457320028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457320028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001457320028 none CN1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 10, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 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, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 27, 13, 27, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 3, 7, 7, 7, 7, 30, 30, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457320028 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028 Building ZINC001457320028 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457320028 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 181) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001457320028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457320028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001457320028 none CN1CCN(C(=O)CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 10, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 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, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 22, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 4, 6, 6, 6, 6, 25, 25, 25, 25] 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: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 182) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001457320028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457320028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001457320028 none CN1CCN(C(=O)CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 10, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 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, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 27, 13, 27, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 3, 7, 7, 7, 7, 30, 30, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457320028 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457320028 Building ZINC001457681000 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457681000 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/183 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)c2ccc(Cl)cc2)cn1) `ZINC001457681000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457681000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457681000 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 11, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 19, 25, 25, 7, 15, 15, 7, 7, 15, 15, 6, 6, 6, 6, 6, 6, 4, 19, 19, 25, 25, 15, 15, 15, 15, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 142 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/184 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)c2ccc(Cl)cc2)cn1) `ZINC001457681000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457681000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457681000 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 11, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 4, 7, 7, 21, 28, 28, 7, 15, 15, 7, 7, 15, 15, 7, 7, 7, 7, 7, 7, 4, 21, 21, 28, 28, 15, 15, 15, 15, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 154 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457681000 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000 Building ZINC001457681000 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457681000 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 183) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)c2ccc(Cl)cc2)cn1) `ZINC001457681000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457681000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457681000 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 11, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 19, 25, 25, 7, 15, 15, 7, 7, 15, 15, 6, 6, 6, 6, 6, 6, 4, 19, 19, 25, 25, 15, 15, 15, 15, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 142 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 184) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)c2ccc(Cl)cc2)cn1) `ZINC001457681000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457681000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457681000 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CC(N)=O)c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 11, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 4, 4, 4, 7, 7, 21, 28, 28, 7, 15, 15, 7, 7, 15, 15, 7, 7, 7, 7, 7, 7, 4, 21, 21, 28, 28, 15, 15, 15, 15, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 154 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457681000 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457681000 Building ZINC001457742163 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457742163 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/185 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1n[nH]c(CNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)n1) `ZINC001457742163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457742163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001457742163 none CCOC(=O)c1n[nH]c(CNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 6, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 20, 46, 20, 20, 20, 20, 12, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 50, 50, 50, 50, 50, 12, 12, 4, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/186 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1n[nH]c(CNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)n1) `ZINC001457742163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457742163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001457742163 none CCOC(=O)c1n[nH]c(CNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 6, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 20, 46, 20, 20, 20, 20, 13, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 50, 50, 50, 50, 50, 13, 13, 4, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457742163 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163 Building ZINC001457742163 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457742163 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 185) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1n[nH]c(CNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)n1) `ZINC001457742163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457742163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001457742163 none CCOC(=O)c1n[nH]c(CNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 6, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 20, 46, 20, 20, 20, 20, 12, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 50, 50, 50, 50, 50, 12, 12, 4, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 186) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1n[nH]c(CNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)n1) `ZINC001457742163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457742163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001457742163 none CCOC(=O)c1n[nH]c(CNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 6, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 20, 46, 20, 20, 20, 20, 13, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 50, 50, 50, 50, 50, 13, 13, 4, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457742163 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457742163 Building ZINC001457874623 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457874623 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/187 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCn1cnc2c1ncnc2N) `ZINC001457874623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457874623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001457874623 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCn1cnc2c1ncnc2N 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', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 17, 17, 22, 22, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/188 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCn1cnc2c1ncnc2N) `ZINC001457874623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457874623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001457874623 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCn1cnc2c1ncnc2N 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', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 17, 17, 22, 22, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457874623 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623 Building ZINC001457874623 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457874623 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 187) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCCn1cnc2c1ncnc2N) `ZINC001457874623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457874623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001457874623 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCn1cnc2c1ncnc2N 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', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 17, 17, 22, 22, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 188) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCCn1cnc2c1ncnc2N) `ZINC001457874623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457874623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001457874623 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCn1cnc2c1ncnc2N 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', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 8, 1, 8, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 17, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 17, 17, 22, 22, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457874623 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457874623 Building ZINC001457950859 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457950859 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/189 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)c1cc(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)ccc1F) `ZINC001457950859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457950859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001457950859 none NS(=O)(=O)c1cc(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)ccc1F NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 50, 50, 34, 34, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 34, 34, 20, 18, 50, 50, 34, 12, 12, 3, 2, 2, 1, 2, 2, 34, 34] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/190 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)c1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)ccc1F) `ZINC001457950859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457950859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001457950859 none NS(=O)(=O)c1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)ccc1F NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 50, 50, 34, 34, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 34, 34, 12, 12, 50, 50, 34, 12, 12, 3, 2, 2, 1, 2, 2, 34, 34] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457950859 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859 Building ZINC001457950859 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457950859 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 189) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)c1cc(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)ccc1F) `ZINC001457950859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457950859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001457950859 none NS(=O)(=O)c1cc(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)ccc1F NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 50, 50, 34, 34, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 34, 34, 20, 18, 50, 50, 34, 12, 12, 3, 2, 2, 1, 2, 2, 34, 34] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 190) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)c1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)ccc1F) `ZINC001457950859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457950859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001457950859 none NS(=O)(=O)c1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)ccc1F NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', '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.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 50, 50, 34, 34, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 34, 34, 12, 12, 50, 50, 34, 12, 12, 3, 2, 2, 1, 2, 2, 34, 34] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001457950859 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001457950859 Building ZINC001458922891 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458922891 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/191 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)C(=O)NC)cn1) `ZINC001458922891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458922891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001458922891 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)C(=O)NC)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.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 14, 14, 14, 14, 14, 14, 6, 11, 11, 11, 6, 6, 22, 22, 22, 22, 22, 6, 3, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 148 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/192 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)C(=O)NC)cn1) `ZINC001458922891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458922891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001458922891 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)C(=O)NC)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.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 6, 6, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 7, 7, 17, 17, 17, 17, 17, 7, 3, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001458922891 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891 Building ZINC001458922891 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458922891 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 191) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](Cc2ccccc2)C(=O)NC)cn1) `ZINC001458922891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458922891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001458922891 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)C(=O)NC)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.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 14, 14, 14, 14, 14, 14, 6, 11, 11, 11, 6, 6, 22, 22, 22, 22, 22, 6, 3, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 148 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 192) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](Cc2ccccc2)C(=O)NC)cn1) `ZINC001458922891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458922891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001458922891 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)C(=O)NC)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.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 6, 6, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 7, 7, 17, 17, 17, 17, 17, 7, 3, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001458922891 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922891 Building ZINC001458922900 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458922900 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/193 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)C(=O)NC)cn1) `ZINC001458922900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458922900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001458922900 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)C(=O)NC)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.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 6, 6, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 7, 7, 17, 17, 17, 17, 17, 7, 3, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/194 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/194' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)C(=O)NC)cn1) `ZINC001458922900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458922900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001458922900 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)C(=O)NC)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.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 13, 13, 13, 13, 13, 13, 6, 10, 10, 10, 6, 6, 21, 21, 21, 21, 21, 6, 3, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001458922900 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900 Building ZINC001458922900 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458922900 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 193) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](Cc2ccccc2)C(=O)NC)cn1) `ZINC001458922900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458922900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001458922900 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)C(=O)NC)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.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 6, 6, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 7, 7, 17, 17, 17, 17, 17, 7, 3, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 194) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](Cc2ccccc2)C(=O)NC)cn1) `ZINC001458922900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458922900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001458922900 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)C(=O)NC)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.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 13, 13, 13, 13, 13, 13, 6, 10, 10, 10, 6, 6, 21, 21, 21, 21, 21, 6, 3, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001458922900 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458922900 Building ZINC001458960278 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458960278 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/195 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H](COC)C(=O)OCC) `ZINC001458960278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458960278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001458960278 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H](COC)C(=O)OCC 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.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 12, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 1, 1, 4, 10, 1, 9, 9, 9, 18, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 4, 4, 1, 4, 4, 10, 10, 10, 18, 18, 18, 18, 18] 35 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 20, 38] set([0, 1, 13, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/196 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/196' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H](COC)C(=O)OCC) `ZINC001458960278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458960278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001458960278 none CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H](COC)C(=O)OCC 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.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 12, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 2, 2, 9, 17, 2, 9, 9, 9, 14, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 1, 9, 9, 17, 17, 17, 14, 14, 14, 14, 14] 50 rigid atoms, others: [32, 4, 38, 6, 7, 8, 9, 10, 11, 12, 14] set([0, 1, 2, 3, 5, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001458960278 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278 Building ZINC001458960278 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458960278 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 195) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC)c1)[C@H](COC)C(=O)OCC) `ZINC001458960278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458960278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001458960278 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@H](COC)C(=O)OCC 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.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 12, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 1, 1, 4, 10, 1, 9, 9, 9, 18, 3, 3, 3, 3, 3, 3, 3, 1, 4, 4, 4, 4, 4, 1, 4, 4, 10, 10, 10, 18, 18, 18, 18, 18] 35 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 20, 38] set([0, 1, 13, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 196) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC)c1)[C@H](COC)C(=O)OCC) `ZINC001458960278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458960278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001458960278 none CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@H](COC)C(=O)OCC 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.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 12, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 2, 2, 9, 17, 2, 9, 9, 9, 14, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 1, 9, 9, 17, 17, 17, 14, 14, 14, 14, 14] 50 rigid atoms, others: [32, 4, 38, 6, 7, 8, 9, 10, 11, 12, 14] set([0, 1, 2, 3, 5, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001458960278 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960278 Building ZINC001458960281 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458960281 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/197 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](COC)C(=O)OCC) `ZINC001458960281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458960281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001458960281 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](COC)C(=O)OCC 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.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 12, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 2, 2, 9, 17, 2, 9, 9, 9, 14, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 1, 9, 9, 17, 17, 17, 14, 14, 14, 14, 14] 50 rigid atoms, others: [32, 4, 38, 6, 7, 8, 9, 10, 11, 12, 14] set([0, 1, 2, 3, 5, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/198 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/198' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](COC)C(=O)OCC) `ZINC001458960281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458960281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001458960281 none CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](COC)C(=O)OCC 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.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 12, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 4, 10, 1, 9, 9, 9, 16, 2, 2, 2, 2, 2, 2, 2, 1, 3, 3, 3, 3, 3, 1, 4, 4, 10, 10, 10, 16, 16, 16, 16, 16] 30 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 20, 38] set([0, 1, 13, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001458960281 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281 Building ZINC001458960281 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458960281 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 197) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC)c1)[C@@H](COC)C(=O)OCC) `ZINC001458960281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458960281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001458960281 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](COC)C(=O)OCC 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.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 12, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2, 2, 2, 9, 17, 2, 9, 9, 9, 14, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 1, 9, 9, 17, 17, 17, 14, 14, 14, 14, 14] 50 rigid atoms, others: [32, 4, 38, 6, 7, 8, 9, 10, 11, 12, 14] set([0, 1, 2, 3, 5, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 198) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC)c1)[C@@H](COC)C(=O)OCC) `ZINC001458960281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458960281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001458960281 none CCCN(C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)[C@@H](COC)C(=O)OCC 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.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 7, 5, 12, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 4, 10, 1, 9, 9, 9, 16, 2, 2, 2, 2, 2, 2, 2, 1, 3, 3, 3, 3, 3, 1, 4, 4, 10, 10, 10, 16, 16, 16, 16, 16] 30 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 20, 38] set([0, 1, 13, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001458960281 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001458960281 Building ZINC001460078218 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460078218 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/199 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)c(S(C)(=O)=O)c2)cn1) `ZINC001460078218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460078218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001460078218 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)c(S(C)(=O)=O)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 14, 5, 11, 11, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 14, 14, 4, 9, 14, 14, 33, 33, 33, 14, 8, 8, 8, 8, 8, 8, 3, 14, 14, 33, 33, 33, 14, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/200 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/200' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)c(S(C)(=O)=O)c2)cn1) `ZINC001460078218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460078218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001460078218 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)c(S(C)(=O)=O)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 14, 5, 11, 11, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 32, 32, 32, 14, 6, 6, 6, 6, 6, 6, 3, 14, 14, 32, 32, 32, 14, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001460078218 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218 Building ZINC001460078218 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460078218 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 199) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)c(S(C)(=O)=O)c2)cn1) `ZINC001460078218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460078218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001460078218 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)c(S(C)(=O)=O)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 14, 5, 11, 11, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 14, 14, 4, 9, 14, 14, 33, 33, 33, 14, 8, 8, 8, 8, 8, 8, 3, 14, 14, 33, 33, 33, 14, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 200) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)c(S(C)(=O)=O)c2)cn1) `ZINC001460078218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460078218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001460078218 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)c(S(C)(=O)=O)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 14, 5, 11, 11, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 32, 32, 32, 14, 6, 6, 6, 6, 6, 6, 3, 14, 14, 32, 32, 32, 14, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001460078218 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460078218 Building ZINC001460264118 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460264118 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/201 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1) `ZINC001460264118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460264118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001460264118 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 3, 8, 8, 5, 8, 14, 14, 8, 8, 8, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 3, 8, 8, 14, 14, 8, 21, 21, 21, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/202 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1) `ZINC001460264118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460264118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001460264118 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 15, 15, 9, 9, 9, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 4, 9, 9, 15, 15, 9, 21, 21, 21, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001460264118 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118 Building ZINC001460264118 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460264118 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 201) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1) `ZINC001460264118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460264118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001460264118 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 3, 8, 8, 5, 8, 14, 14, 8, 8, 8, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 3, 8, 8, 14, 14, 8, 21, 21, 21, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 202) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1) `ZINC001460264118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460264118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001460264118 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 15, 15, 9, 9, 9, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 4, 9, 9, 15, 15, 9, 21, 21, 21, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001460264118 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460264118 Building ZINC001460800906 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460800906 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/203 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1[nH]nnc1C(=O)NC1CC1) `ZINC001460800906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460800906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001460800906 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1[nH]nnc1C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.pl3', 'H', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 6, 8, 8, 1, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 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] 0 hydrogens need rotated 50 conformations 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, 14, 14, 14, 14, 14, 14, 35, 35, 35, 48, 48, 4, 4, 4, 4, 4, 4, 4, 10, 35, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/204 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1[nH]nnc1C(=O)NC1CC1) `ZINC001460800906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460800906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001460800906 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1[nH]nnc1C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.pl3', 'H', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 6, 8, 8, 1, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 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] 0 hydrogens need rotated 50 conformations 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, 14, 14, 14, 14, 14, 14, 35, 35, 35, 48, 48, 4, 4, 4, 4, 4, 4, 4, 10, 35, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001460800906 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906 Building ZINC001460800906 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460800906 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 203) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1[nH]nnc1C(=O)NC1CC1) `ZINC001460800906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460800906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001460800906 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1[nH]nnc1C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.pl3', 'H', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 6, 8, 8, 1, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 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] 0 hydrogens need rotated 50 conformations 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, 14, 14, 14, 14, 14, 14, 35, 35, 35, 48, 48, 4, 4, 4, 4, 4, 4, 4, 10, 35, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 204) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/204: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc1[nH]nnc1C(=O)NC1CC1) `ZINC001460800906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460800906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001460800906 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1[nH]nnc1C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.pl3', 'H', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 6, 8, 8, 1, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 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] 0 hydrogens need rotated 50 conformations 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, 14, 14, 14, 14, 14, 14, 35, 35, 35, 48, 48, 4, 4, 4, 4, 4, 4, 4, 10, 35, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001460800906 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460800906 Building ZINC001460927553 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460927553 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/205 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1S(C)(=O)=O) `ZINC001460927553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460927553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001460927553 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8] 11 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 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: 31 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/206 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1S(C)(=O)=O) `ZINC001460927553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460927553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001460927553 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8] 11 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 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: 31 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001460927553 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553 Building ZINC001460927553 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460927553 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 205) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/205: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1S(C)(=O)=O) `ZINC001460927553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460927553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001460927553 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8] 11 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 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: 31 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 206) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1S(C)(=O)=O) `ZINC001460927553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460927553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001460927553 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8] 11 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 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: 31 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001460927553 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001460927553 Building ZINC001461370917 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461370917 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/207 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nnc2n1CCN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C2) `ZINC001461370917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461370917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001461370917 none COCc1nnc2n1CCN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 23, 6, 6, 6, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 6, 32, 32, 32, 23, 23, 6, 6, 6, 6, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 6, 6] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/208 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nnc2n1CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C2) `ZINC001461370917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461370917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001461370917 none COCc1nnc2n1CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 5, 29, 29, 29, 19, 19, 5, 5, 5, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 5, 5] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001461370917 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917 Building ZINC001461370917 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461370917 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 207) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nnc2n1CCN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C2) `ZINC001461370917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461370917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001461370917 none COCc1nnc2n1CCN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 23, 6, 6, 6, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 6, 32, 32, 32, 23, 23, 6, 6, 6, 6, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 6, 6] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 208) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nnc2n1CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C2) `ZINC001461370917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461370917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001461370917 none COCc1nnc2n1CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 5, 29, 29, 29, 19, 19, 5, 5, 5, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 5, 5] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001461370917 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461370917 Building ZINC001461546427 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461546427 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/209 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)nc2n1CCC2) `ZINC001461546427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461546427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461546427 none COC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)nc2n1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 15, 32, 15, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 49 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/210 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)nc2n1CCC2) `ZINC001461546427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461546427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461546427 none COC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)nc2n1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 15, 29, 15, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 29, 29, 29, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15] 45 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: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001461546427 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427 Building ZINC001461546427 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461546427 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 209) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)nc2n1CCC2) `ZINC001461546427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461546427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461546427 none COC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)nc2n1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 15, 32, 15, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 49 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 210) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)nc2n1CCC2) `ZINC001461546427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461546427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461546427 none COC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)nc2n1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 15, 29, 15, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 29, 29, 29, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15] 45 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: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001461546427 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001461546427 Building ZINC001462008896 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462008896 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/211 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001462008896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462008896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001462008896 none COC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 23, 42, 12, 23, 23, 12, 6, 12, 2, 6, 6, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 42, 42, 42, 23, 23, 23, 12, 6, 6, 6, 2, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/212 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/212' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001462008896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462008896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001462008896 none COC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 38, 12, 20, 20, 12, 6, 12, 3, 6, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 20, 20, 20, 12, 6, 6, 6, 3, 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001462008896 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896 Building ZINC001462008896 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462008896 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 211) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001462008896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462008896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001462008896 none COC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 23, 42, 12, 23, 23, 12, 6, 12, 2, 6, 6, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 42, 42, 42, 23, 23, 23, 12, 6, 6, 6, 2, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 212) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001462008896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462008896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001462008896 none COC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 38, 12, 20, 20, 12, 6, 12, 3, 6, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 20, 20, 20, 12, 6, 6, 6, 3, 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001462008896 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462008896 Building ZINC001462340962 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462340962 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/213 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2c2nnnn2C)cn1) `ZINC001462340962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462340962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001462340962 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2c2nnnn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 9, 9, 17, 17, 17, 17, 17, 9, 5, 10, 10, 10, 10, 16, 16, 16, 9] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/214 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2c2nnnn2C)cn1) `ZINC001462340962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462340962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001462340962 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2c2nnnn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 9, 9, 17, 17, 17, 17, 17, 9, 5, 10, 10, 10, 10, 16, 16, 16, 9] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001462340962 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962 Building ZINC001462340962 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462340962 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 213) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2ccccc2c2nnnn2C)cn1) `ZINC001462340962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462340962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001462340962 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2c2nnnn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 9, 9, 17, 17, 17, 17, 17, 9, 5, 10, 10, 10, 10, 16, 16, 16, 9] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 214) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2ccccc2c2nnnn2C)cn1) `ZINC001462340962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462340962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001462340962 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2c2nnnn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 9, 9, 17, 17, 17, 17, 17, 9, 5, 10, 10, 10, 10, 16, 16, 16, 9] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001462340962 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462340962 Building ZINC001462801092 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462801092 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/215 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)n(C)ccn23)c1) `ZINC001462801092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462801092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001462801092 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)n(C)ccn23)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 8, 8, 1, 1, 1, 1, 5, 5, 5, 17, 22, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 2, 8, 8, 5, 17, 17, 22, 22, 27, 27, 27, 27, 27, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/216 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)n(C)ccn23)c1) `ZINC001462801092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462801092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001462801092 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)n(C)ccn23)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 7, 7, 1, 1, 1, 1, 5, 5, 5, 17, 22, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 2, 7, 7, 5, 17, 17, 22, 22, 27, 27, 27, 27, 27, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001462801092 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092 Building ZINC001462801092 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462801092 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 215) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)n(C)ccn23)c1) `ZINC001462801092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462801092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001462801092 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)n(C)ccn23)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 8, 8, 1, 1, 1, 1, 5, 5, 5, 17, 22, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 2, 8, 8, 5, 17, 17, 22, 22, 27, 27, 27, 27, 27, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 216) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)n(C)ccn23)c1) `ZINC001462801092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462801092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001462801092 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)n(C)ccn23)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 7, 7, 1, 1, 1, 1, 5, 5, 5, 17, 22, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 2, 7, 7, 5, 17, 17, 22, 22, 27, 27, 27, 27, 27, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001462801092 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462801092 Building ZINC001462822570 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462822570 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/217 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)N=S(C)(C)=O)c1) `ZINC001462822570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462822570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001462822570 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)N=S(C)(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'C.3', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 8, 14, 5, 5, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 15, 25, 25, 25, 28, 28, 28, 28, 6, 6, 6, 6, 2, 6, 6, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/218 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)N=S(C)(C)=O)c1) `ZINC001462822570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462822570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001462822570 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)N=S(C)(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'C.3', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 8, 14, 5, 5, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 17, 21, 21, 21, 28, 28, 28, 28, 6, 6, 6, 6, 2, 6, 6, 3, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001462822570 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570 Building ZINC001462822570 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462822570 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 217) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)N=S(C)(C)=O)c1) `ZINC001462822570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462822570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001462822570 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCS(=O)(=O)N=S(C)(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'C.3', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 8, 14, 5, 5, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 15, 25, 25, 25, 28, 28, 28, 28, 6, 6, 6, 6, 2, 6, 6, 3, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 218) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)N=S(C)(C)=O)c1) `ZINC001462822570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462822570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001462822570 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCS(=O)(=O)N=S(C)(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'C.3', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 8, 14, 5, 5, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 17, 17, 21, 21, 21, 28, 28, 28, 28, 6, 6, 6, 6, 2, 6, 6, 3, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001462822570 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462822570 Building ZINC001462823230 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462823230 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/219 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nnc2c(=O)[nH]ccn12)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001462823230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462823230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001462823230 none O=C(NCc1nnc2c(=O)[nH]ccn12)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 22, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 8, 8, 8, 8, 8, 4, 22, 22, 34, 34, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/220 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nnc2c(=O)[nH]ccn12)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001462823230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462823230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001462823230 none O=C(NCc1nnc2c(=O)[nH]ccn12)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 22, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 8, 8, 8, 8, 8, 4, 22, 22, 34, 34, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001462823230 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230 Building ZINC001462823230 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462823230 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 219) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nnc2c(=O)[nH]ccn12)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001462823230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462823230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001462823230 none O=C(NCc1nnc2c(=O)[nH]ccn12)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 22, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 8, 8, 8, 8, 8, 4, 22, 22, 34, 34, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 220) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nnc2c(=O)[nH]ccn12)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001462823230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462823230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001462823230 none O=C(NCc1nnc2c(=O)[nH]ccn12)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 22, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 8, 8, 8, 8, 8, 4, 22, 22, 34, 34, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001462823230 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462823230 Building ZINC001462924185 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462924185 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/221 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)CNS(C)(=O)=O)cn1) `ZINC001462924185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462924185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001462924185 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 7, 7, 7, 17, 30, 37, 37, 37, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 3, 7, 7, 7, 7, 7, 7, 17, 17, 30, 37, 37, 37, 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]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/222 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)CNS(C)(=O)=O)cn1) `ZINC001462924185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462924185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001462924185 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 18, 31, 38, 38, 38, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 3, 8, 8, 8, 8, 8, 8, 18, 18, 31, 38, 38, 38, 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]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001462924185 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185 Building ZINC001462924185 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462924185 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 221) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC(C)(C)CNS(C)(=O)=O)cn1) `ZINC001462924185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462924185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001462924185 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC(C)(C)CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 7, 7, 7, 17, 30, 37, 37, 37, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 3, 7, 7, 7, 7, 7, 7, 17, 17, 30, 37, 37, 37, 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]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 222) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC(C)(C)CNS(C)(=O)=O)cn1) `ZINC001462924185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462924185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001462924185 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC(C)(C)CNS(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 18, 31, 38, 38, 38, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 3, 8, 8, 8, 8, 8, 8, 18, 18, 31, 38, 38, 38, 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]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001462924185 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001462924185 Building ZINC001463071141 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463071141 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/223 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCCONC(=O)OC(C)(C)C)cn1) `ZINC001463071141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463071141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001463071141 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCCONC(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 22, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/224 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCONC(=O)OC(C)(C)C)cn1) `ZINC001463071141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463071141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001463071141 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCONC(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 25, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001463071141 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141 Building ZINC001463071141 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463071141 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 223) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCCONC(=O)OC(C)(C)C)cn1) `ZINC001463071141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463071141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001463071141 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCCONC(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 22, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 224) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCONC(=O)OC(C)(C)C)cn1) `ZINC001463071141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463071141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001463071141 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCONC(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 25, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001463071141 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463071141 Building ZINC001463408505 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463408505 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/225 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3C(=O)CCC3=O)cc2)cn1) `ZINC001463408505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463408505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001463408505 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3C(=O)CCC3=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 18, 18, 6, 6, 31, 31, 31, 31, 29, 31, 18, 18, 12, 12, 12, 12, 12, 12, 6, 18, 18, 31, 31, 31, 31, 18, 18, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/226 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3C(=O)CCC3=O)cc2)cn1) `ZINC001463408505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463408505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001463408505 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3C(=O)CCC3=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 15, 15, 10, 15, 35, 35, 35, 35, 35, 35, 15, 15, 12, 12, 12, 12, 12, 12, 6, 15, 15, 35, 35, 35, 35, 15, 15, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001463408505 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505 Building ZINC001463408505 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463408505 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 225) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3C(=O)CCC3=O)cc2)cn1) `ZINC001463408505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463408505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001463408505 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3C(=O)CCC3=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 18, 18, 6, 6, 31, 31, 31, 31, 29, 31, 18, 18, 12, 12, 12, 12, 12, 12, 6, 18, 18, 31, 31, 31, 31, 18, 18, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 226) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3C(=O)CCC3=O)cc2)cn1) `ZINC001463408505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463408505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001463408505 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3C(=O)CCC3=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 15, 15, 10, 15, 35, 35, 35, 35, 35, 35, 15, 15, 12, 12, 12, 12, 12, 12, 6, 15, 15, 35, 35, 35, 35, 15, 15, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001463408505 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463408505 Building ZINC001463526679 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463526679 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/227 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c2ccccc12) `ZINC001463526679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463526679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001463526679 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 17, 17, 5, 4, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/228 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/228' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1n[nH]c2ccccc12) `ZINC001463526679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463526679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001463526679 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1n[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 17, 17, 5, 4, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001463526679 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679 Building ZINC001463526679 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463526679 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 227) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c2ccccc12) `ZINC001463526679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463526679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001463526679 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 17, 17, 5, 4, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 228) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1n[nH]c2ccccc12) `ZINC001463526679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463526679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001463526679 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1n[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 17, 17, 5, 4, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001463526679 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463526679 Building ZINC001463620768 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463620768 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/229 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1F) `ZINC001463620768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463620768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001463620768 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 19, 19, 5, 3, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/230 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1F) `ZINC001463620768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463620768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001463620768 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 3, 3, 3, 10, 10, 8, 10, 10, 10, 10, 5, 5, 5, 5, 19, 19, 5, 3, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001463620768 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768 Building ZINC001463620768 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463620768 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 229) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1F) `ZINC001463620768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463620768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001463620768 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 19, 19, 5, 3, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 230) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1F) `ZINC001463620768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463620768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001463620768 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 19, 19, 19, 5, 1, 1, 1, 1, 3, 3, 3, 10, 10, 8, 10, 10, 10, 10, 5, 5, 5, 5, 19, 19, 5, 3, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001463620768 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463620768 Building ZINC001463890726 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463890726 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/231 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCOc2ccccc21) `ZINC001463890726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463890726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001463890726 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCOc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 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: [6, 6, 6, 6, 6, 24, 24, 24, 6, 1, 1, 1, 2, 8, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 24, 24, 6, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/232 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCOc2ccccc21) `ZINC001463890726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463890726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001463890726 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCOc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 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: [6, 6, 6, 6, 6, 24, 24, 24, 6, 1, 1, 1, 2, 7, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 24, 24, 6, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001463890726 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726 Building ZINC001463890726 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463890726 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 231) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCOc2ccccc21) `ZINC001463890726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463890726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001463890726 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCOc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 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: [6, 6, 6, 6, 6, 24, 24, 24, 6, 1, 1, 1, 2, 8, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 24, 24, 6, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 232) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCOc2ccccc21) `ZINC001463890726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463890726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001463890726 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCOc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 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: [6, 6, 6, 6, 6, 24, 24, 24, 6, 1, 1, 1, 2, 7, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 24, 24, 6, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001463890726 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001463890726 Building ZINC001464103470 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464103470 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/233 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1) `ZINC001464103470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464103470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001464103470 none NC(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 12, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 19, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 28, 28, 19, 19, 5, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 100 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/234 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1) `ZINC001464103470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464103470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001464103470 none NC(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 12, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 19, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 28, 28, 19, 19, 4, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 104 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464103470 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470 Building ZINC001464103470 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464103470 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 233) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1) `ZINC001464103470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464103470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001464103470 none NC(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 12, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 19, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 28, 28, 19, 19, 5, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 100 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 234) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1) `ZINC001464103470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464103470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001464103470 none NC(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CCOCC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 12, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 19, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 28, 28, 19, 19, 4, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 104 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464103470 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464103470 Building ZINC001464326859 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464326859 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/235 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(F)cc1) `ZINC001464326859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464326859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001464326859 none CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 16, 16, 16, 5, 5, 5, 7, 12, 12, 9, 10, 12, 12, 7, 7, 7, 5, 16, 16, 5, 5, 5, 5, 12, 12, 12, 12] 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]) total number of confs: 87 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/236 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(F)cc1) `ZINC001464326859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464326859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001464326859 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 15, 15, 15, 4, 4, 4, 6, 12, 12, 9, 11, 12, 12, 6, 6, 6, 4, 15, 15, 4, 4, 4, 4, 12, 12, 12, 12] 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]) total number of confs: 88 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464326859 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859 Building ZINC001464326859 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464326859 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 235) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(F)cc1) `ZINC001464326859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464326859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001464326859 none CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 16, 16, 16, 5, 5, 5, 7, 12, 12, 9, 10, 12, 12, 7, 7, 7, 5, 16, 16, 5, 5, 5, 5, 12, 12, 12, 12] 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]) total number of confs: 87 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 236) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(F)cc1) `ZINC001464326859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464326859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001464326859 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 15, 15, 15, 4, 4, 4, 6, 12, 12, 9, 11, 12, 12, 6, 6, 6, 4, 15, 15, 4, 4, 4, 4, 12, 12, 12, 12] 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]) total number of confs: 88 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464326859 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464326859 Building ZINC001464904006 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464904006 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/237 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001464904006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464904006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001464904006 none NC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 20, 20, 20, 7, 20, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 20, 28, 28, 20, 20, 20, 20, 4, 9, 9, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/238 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001464904006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464904006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001464904006 none NC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 33, 23, 23, 23, 8, 23, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 23, 33, 33, 23, 23, 23, 23, 5, 10, 10, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464904006 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006 Building ZINC001464904006 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464904006 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 237) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001464904006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464904006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001464904006 none NC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 20, 20, 20, 7, 20, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 20, 28, 28, 20, 20, 20, 20, 4, 9, 9, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 238) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001464904006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464904006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001464904006 none NC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 33, 23, 23, 23, 8, 23, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 23, 33, 33, 23, 23, 23, 23, 5, 10, 10, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464904006 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904006 Building ZINC001464904002 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464904002 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/239 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001464904002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464904002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001464904002 none NC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 23, 32, 23, 23, 23, 8, 23, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 23, 32, 32, 23, 23, 23, 23, 5, 10, 10, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/240 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001464904002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464904002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001464904002 none NC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 20, 20, 20, 7, 20, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 20, 28, 28, 20, 20, 20, 20, 4, 9, 9, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464904002 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002 Building ZINC001464904002 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464904002 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 239) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001464904002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464904002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001464904002 none NC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 23, 32, 23, 23, 23, 8, 23, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 23, 32, 32, 23, 23, 23, 23, 5, 10, 10, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 240) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001464904002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464904002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001464904002 none NC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 20, 20, 20, 7, 20, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 20, 28, 28, 20, 20, 20, 20, 4, 9, 9, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464904002 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464904002 Building ZINC001464929054 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464929054 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/241 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 32, 16, 16, 16, 16, 16, 7, 16, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 32, 32, 25, 25, 16, 16, 16, 16, 16, 16, 3, 5, 5, 5, 5, 16, 16] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/242 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 34, 18, 18, 18, 18, 18, 7, 18, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 34, 34, 29, 29, 18, 18, 18, 18, 18, 18, 3, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/243 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/243' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 32, 16, 16, 16, 16, 16, 7, 16, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 32, 32, 25, 25, 16, 16, 16, 16, 16, 16, 3, 5, 5, 5, 5, 16, 16] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/244 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/244' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 34, 18, 18, 18, 18, 18, 7, 18, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 34, 34, 29, 29, 18, 18, 18, 18, 18, 18, 3, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464929054 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 Building ZINC001464929054 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464929054 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 241) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 32, 16, 16, 16, 16, 16, 7, 16, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 32, 32, 25, 25, 16, 16, 16, 16, 16, 16, 3, 5, 5, 5, 5, 16, 16] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 242) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 34, 18, 18, 18, 18, 18, 7, 18, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 34, 34, 29, 29, 18, 18, 18, 18, 18, 18, 3, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 243) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 32, 16, 16, 16, 16, 16, 7, 16, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 32, 32, 25, 25, 16, 16, 16, 16, 16, 16, 3, 5, 5, 5, 5, 16, 16] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 244) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 34, 18, 18, 18, 18, 18, 7, 18, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 34, 34, 29, 29, 18, 18, 18, 18, 18, 18, 3, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464929054 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 Building ZINC001464929054 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464929054 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 241) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 32, 16, 16, 16, 16, 16, 7, 16, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 32, 32, 25, 25, 16, 16, 16, 16, 16, 16, 3, 5, 5, 5, 5, 16, 16] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 242) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 34, 18, 18, 18, 18, 18, 7, 18, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 34, 34, 29, 29, 18, 18, 18, 18, 18, 18, 3, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 243) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 32, 16, 16, 16, 16, 16, 7, 16, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 32, 32, 25, 25, 16, 16, 16, 16, 16, 16, 3, 5, 5, 5, 5, 16, 16] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 244) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 34, 18, 18, 18, 18, 18, 7, 18, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 34, 34, 29, 29, 18, 18, 18, 18, 18, 18, 3, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464929054 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 Building ZINC001464929054 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464929054 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 241) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 32, 16, 16, 16, 16, 16, 7, 16, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 32, 32, 25, 25, 16, 16, 16, 16, 16, 16, 3, 5, 5, 5, 5, 16, 16] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 242) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 34, 18, 18, 18, 18, 18, 7, 18, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 34, 34, 29, 29, 18, 18, 18, 18, 18, 18, 3, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 243) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 32, 16, 16, 16, 16, 16, 7, 16, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 32, 32, 25, 25, 16, 16, 16, 16, 16, 16, 3, 5, 5, 5, 5, 16, 16] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 244) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929054.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464929054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929054 none NC(=O)CN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 34, 18, 18, 18, 18, 18, 7, 18, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 34, 34, 29, 29, 18, 18, 18, 18, 18, 18, 3, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464929054 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929054 Building ZINC001464929079 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464929079 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/245 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 31, 16, 16, 16, 16, 16, 6, 16, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 31, 31, 28, 28, 16, 16, 16, 16, 16, 16, 3, 4, 4, 4, 4, 16, 16] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/246 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 31, 14, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 31, 31, 24, 24, 14, 14, 14, 14, 14, 14, 3, 5, 5, 5, 5, 14, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/247 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/247' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 31, 16, 16, 16, 16, 16, 6, 16, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 31, 31, 28, 28, 16, 16, 16, 16, 16, 16, 3, 4, 4, 4, 4, 16, 16] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/248 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/248' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 31, 14, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 31, 31, 24, 24, 14, 14, 14, 14, 14, 14, 3, 5, 5, 5, 5, 14, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464929079 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 Building ZINC001464929079 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464929079 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 245) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 31, 16, 16, 16, 16, 16, 6, 16, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 31, 31, 28, 28, 16, 16, 16, 16, 16, 16, 3, 4, 4, 4, 4, 16, 16] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 246) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 31, 14, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 31, 31, 24, 24, 14, 14, 14, 14, 14, 14, 3, 5, 5, 5, 5, 14, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 247) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 31, 16, 16, 16, 16, 16, 6, 16, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 31, 31, 28, 28, 16, 16, 16, 16, 16, 16, 3, 4, 4, 4, 4, 16, 16] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 248) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 31, 14, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 31, 31, 24, 24, 14, 14, 14, 14, 14, 14, 3, 5, 5, 5, 5, 14, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464929079 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 Building ZINC001464929079 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464929079 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 245) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 31, 16, 16, 16, 16, 16, 6, 16, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 31, 31, 28, 28, 16, 16, 16, 16, 16, 16, 3, 4, 4, 4, 4, 16, 16] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 246) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 31, 14, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 31, 31, 24, 24, 14, 14, 14, 14, 14, 14, 3, 5, 5, 5, 5, 14, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 247) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 31, 16, 16, 16, 16, 16, 6, 16, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 31, 31, 28, 28, 16, 16, 16, 16, 16, 16, 3, 4, 4, 4, 4, 16, 16] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 248) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 31, 14, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 31, 31, 24, 24, 14, 14, 14, 14, 14, 14, 3, 5, 5, 5, 5, 14, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464929079 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 Building ZINC001464929079 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464929079 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 245) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 31, 16, 16, 16, 16, 16, 6, 16, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 31, 31, 28, 28, 16, 16, 16, 16, 16, 16, 3, 4, 4, 4, 4, 16, 16] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 246) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 31, 14, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 31, 31, 24, 24, 14, 14, 14, 14, 14, 14, 3, 5, 5, 5, 5, 14, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 247) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 31, 16, 16, 16, 16, 16, 6, 16, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 31, 31, 28, 28, 16, 16, 16, 16, 16, 16, 3, 4, 4, 4, 4, 16, 16] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 248) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001464929079.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464929079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464929079 none NC(=O)CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 31, 14, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 31, 31, 24, 24, 14, 14, 14, 14, 14, 14, 3, 5, 5, 5, 5, 14, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464929079 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464929079 Building ZINC001464930576 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464930576 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/249 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 33, 21, 21, 21, 21, 21, 9, 1, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 33, 33, 31, 31, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 21, 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/250 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/250' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 19, 19, 19, 19, 19, 8, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 31, 31, 30, 30, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/251 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/251' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 33, 21, 21, 21, 21, 21, 9, 1, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 33, 33, 31, 31, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 21, 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/252 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/252' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 19, 19, 19, 19, 19, 8, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 31, 31, 30, 30, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464930576 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 Building ZINC001464930576 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464930576 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 249) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 33, 21, 21, 21, 21, 21, 9, 1, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 33, 33, 31, 31, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 21, 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 250) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 19, 19, 19, 19, 19, 8, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 31, 31, 30, 30, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 251) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 33, 21, 21, 21, 21, 21, 9, 1, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 33, 33, 31, 31, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 21, 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 252) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 19, 19, 19, 19, 19, 8, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 31, 31, 30, 30, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464930576 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 Building ZINC001464930576 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464930576 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 249) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 33, 21, 21, 21, 21, 21, 9, 1, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 33, 33, 31, 31, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 21, 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 250) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 19, 19, 19, 19, 19, 8, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 31, 31, 30, 30, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 251) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 33, 21, 21, 21, 21, 21, 9, 1, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 33, 33, 31, 31, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 21, 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 252) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 19, 19, 19, 19, 19, 8, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 31, 31, 30, 30, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464930576 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 Building ZINC001464930576 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464930576 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 249) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 33, 21, 21, 21, 21, 21, 9, 1, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 33, 33, 31, 31, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 21, 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 250) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 19, 19, 19, 19, 19, 8, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 31, 31, 30, 30, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 251) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 33, 21, 21, 21, 21, 21, 9, 1, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 33, 33, 31, 31, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 21, 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 252) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464930576.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464930576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001464930576 none NC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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: [8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 19, 19, 19, 19, 19, 8, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 31, 31, 30, 30, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001464930576 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001464930576 Building ZINC001466362849 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466362849 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/253 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1cc[nH]n1) `ZINC001466362849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466362849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466362849 none O=C(NCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1cc[nH]n1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 6, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 21, 21, 15, 15, 3, 4, 4, 4, 4, 30, 30] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/254 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1cc[nH]n1) `ZINC001466362849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466362849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466362849 none O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1cc[nH]n1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 6, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 21, 21, 15, 15, 3, 4, 4, 4, 4, 30, 30] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001466362849 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849 Building ZINC001466362849 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466362849 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 253) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1cc[nH]n1) `ZINC001466362849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466362849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466362849 none O=C(NCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1cc[nH]n1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 6, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 21, 21, 15, 15, 3, 4, 4, 4, 4, 30, 30] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 254) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1cc[nH]n1) `ZINC001466362849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466362849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466362849 none O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1cc[nH]n1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 6, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 21, 21, 15, 15, 3, 4, 4, 4, 4, 30, 30] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001466362849 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466362849 Building ZINC001466865077 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466865077 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/255 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc[nH]n2)CC1) `ZINC001466865077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466865077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001466865077 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc[nH]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.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 8, 6, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number 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, 7, 9, 9, 9, 9, 12, 12, 12, 18, 18, 18, 18, 18, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/256 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc[nH]n2)CC1) `ZINC001466865077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466865077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001466865077 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc[nH]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.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 8, 6, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number 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, 10, 10, 10, 10, 12, 12, 12, 20, 20, 20, 20, 20, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 20, 20, 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001466865077 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077 Building ZINC001466865077 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466865077 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 255) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc[nH]n2)CC1) `ZINC001466865077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466865077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001466865077 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc[nH]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.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 8, 6, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number 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, 7, 9, 9, 9, 9, 12, 12, 12, 18, 18, 18, 18, 18, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 256) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc[nH]n2)CC1) `ZINC001466865077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466865077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001466865077 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)c2cc[nH]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.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 8, 6, 8, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number 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, 10, 10, 10, 10, 12, 12, 12, 20, 20, 20, 20, 20, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 20, 20, 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001466865077 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466865077 Building ZINC001466954170 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466954170 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/257 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=NO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001466954170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466954170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001466954170 none NC(=O)C1=NO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 35, 28, 28, 28, 20, 28, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 35, 35, 14, 14, 4, 6, 6, 6, 6, 28, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/258 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=NO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001466954170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466954170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001466954170 none NC(=O)C1=NO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 26, 33, 26, 26, 26, 22, 26, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 33, 33, 16, 16, 4, 9, 9, 9, 9, 26, 26] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001466954170 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170 Building ZINC001466954170 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466954170 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 257) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=NO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001466954170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466954170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001466954170 none NC(=O)C1=NO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 35, 28, 28, 28, 20, 28, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 35, 35, 14, 14, 4, 6, 6, 6, 6, 28, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 258) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=NO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001466954170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466954170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001466954170 none NC(=O)C1=NO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 26, 33, 26, 26, 26, 22, 26, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 33, 33, 16, 16, 4, 9, 9, 9, 9, 26, 26] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001466954170 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954170 Building ZINC001466954174 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466954174 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/259 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=NO[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001466954174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466954174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001466954174 none NC(=O)C1=NO[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 34, 27, 27, 27, 23, 27, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 34, 34, 16, 16, 4, 9, 9, 9, 9, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/260 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/260' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=NO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001466954174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466954174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001466954174 none NC(=O)C1=NO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 29, 35, 29, 29, 29, 21, 29, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 35, 35, 15, 15, 4, 6, 6, 6, 6, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001466954174 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174 Building ZINC001466954174 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466954174 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 259) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=NO[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001466954174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466954174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001466954174 none NC(=O)C1=NO[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 34, 27, 27, 27, 23, 27, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 34, 34, 16, 16, 4, 9, 9, 9, 9, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 260) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=NO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001466954174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466954174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001466954174 none NC(=O)C1=NO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 29, 35, 29, 29, 29, 21, 29, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 35, 35, 15, 15, 4, 6, 6, 6, 6, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001466954174 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001466954174 Building ZINC001467273477 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467273477 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/261 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CC(=O)OC)CCS(=O)(=O)CC1) `ZINC001467273477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467273477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001467273477 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CC(=O)OC)CCS(=O)(=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.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 14, 11, 11, 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, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 3, 5, 15, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 15, 15, 18, 18, 18, 5, 5, 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, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/262 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CC(=O)OC)CCS(=O)(=O)CC1) `ZINC001467273477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467273477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001467273477 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CC(=O)OC)CCS(=O)(=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.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 14, 11, 11, 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, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 3, 5, 14, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 17, 17, 17, 5, 5, 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, 43, 44, 45, 46, 47]) total number of confs: 75 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001467273477 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477 Building ZINC001467273477 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467273477 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 261) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CC(=O)OC)CCS(=O)(=O)CC1) `ZINC001467273477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467273477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001467273477 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CC(=O)OC)CCS(=O)(=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.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 14, 11, 11, 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, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 3, 5, 15, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 15, 15, 18, 18, 18, 5, 5, 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, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 262) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CC(=O)OC)CCS(=O)(=O)CC1) `ZINC001467273477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467273477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001467273477 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CC(=O)OC)CCS(=O)(=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.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 14, 11, 11, 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, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 3, 5, 14, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 17, 17, 17, 5, 5, 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, 43, 44, 45, 46, 47]) total number of confs: 75 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001467273477 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467273477 Building ZINC001467456492 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467456492 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/263 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2nn[nH]n2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001467456492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467456492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001467456492 none O=C(N1CCC(O)(c2nn[nH]n2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 8, 8, 8, 6, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 11, 17, 17, 17, 17, 17, 32, 32, 32, 32, 32, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 17, 51, 17, 17, 17, 17, 5, 5] 150 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/264 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/264' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2nn[nH]n2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001467456492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467456492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001467456492 none O=C(N1CCC(O)(c2nn[nH]n2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 8, 8, 8, 6, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 10, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 45, 15, 15, 15, 15, 5, 5] 150 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001467456492 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492 Building ZINC001467456492 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467456492 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 263) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2nn[nH]n2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001467456492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467456492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001467456492 none O=C(N1CCC(O)(c2nn[nH]n2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 8, 8, 8, 6, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 11, 17, 17, 17, 17, 17, 32, 32, 32, 32, 32, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 17, 51, 17, 17, 17, 17, 5, 5] 150 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 264) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2nn[nH]n2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001467456492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467456492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001467456492 none O=C(N1CCC(O)(c2nn[nH]n2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 8, 8, 8, 6, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 10, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 45, 15, 15, 15, 15, 5, 5] 150 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001467456492 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467456492 Building ZINC001467684216 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467684216 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/265 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cscc1CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467684216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467684216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001467684216 none Cc1cscc1CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 19, 19, 19, 19, 19, 11, 11, 3, 2, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/266 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cscc1CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467684216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467684216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001467684216 none Cc1cscc1CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 19, 19, 19, 19, 19, 11, 11, 3, 2, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001467684216 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216 Building ZINC001467684216 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467684216 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 265) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cscc1CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467684216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467684216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001467684216 none Cc1cscc1CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 19, 19, 19, 19, 19, 11, 11, 3, 2, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 266) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cscc1CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001467684216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467684216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001467684216 none Cc1cscc1CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 19, 19, 19, 19, 19, 11, 11, 3, 2, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001467684216 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467684216 Building ZINC001467794518 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467794518 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/267 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c(C(=O)NCCO)n1C) `ZINC001467794518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467794518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001467794518 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c(C(=O)NCCO)n1C NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 12, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 24, 27, 6, 6, 6, 6, 6, 2, 6, 6, 6, 6, 6, 6, 6, 8, 24, 24, 27, 27, 81, 6, 6, 6] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/268 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c(C(=O)NCCO)n1C) `ZINC001467794518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467794518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001467794518 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c(C(=O)NCCO)n1C NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 12, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 6, 8, 8, 8, 25, 28, 6, 6, 6, 6, 6, 2, 6, 6, 2, 6, 6, 6, 6, 8, 25, 25, 28, 28, 84, 6, 6, 6] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 207 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001467794518 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518 Building ZINC001467794518 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467794518 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 267) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c(C(=O)NCCO)n1C) `ZINC001467794518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467794518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001467794518 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c(C(=O)NCCO)n1C NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 12, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 24, 27, 6, 6, 6, 6, 6, 2, 6, 6, 6, 6, 6, 6, 6, 8, 24, 24, 27, 27, 81, 6, 6, 6] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 268) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c(C(=O)NCCO)n1C) `ZINC001467794518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467794518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001467794518 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c(C(=O)NCCO)n1C NO_LONG_NAME dock atom types: ['C.3', '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.3', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 12, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 6, 8, 8, 8, 25, 28, 6, 6, 6, 6, 6, 2, 6, 6, 2, 6, 6, 6, 6, 8, 25, 25, 28, 28, 84, 6, 6, 6] 150 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 207 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001467794518 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001467794518 Building ZINC001468298591 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468298591 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/269 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C3CC(=O)NC(=O)C3)c2)cn1) `ZINC001468298591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468298591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001468298591 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C3CC(=O)NC(=O)C3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 11, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 12, 12, 36, 36, 36, 36, 36, 36, 36, 12, 6, 6, 6, 6, 6, 6, 2, 12, 12, 12, 36, 36, 36, 36, 36, 36, 12, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/270 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/270' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C3CC(=O)NC(=O)C3)c2)cn1) `ZINC001468298591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468298591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001468298591 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C3CC(=O)NC(=O)C3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 11, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 12, 2, 12, 12, 35, 35, 35, 35, 35, 35, 35, 12, 6, 6, 6, 6, 6, 6, 2, 12, 12, 8, 35, 35, 35, 35, 35, 35, 12, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468298591 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591 Building ZINC001468298591 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468298591 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 269) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C3CC(=O)NC(=O)C3)c2)cn1) `ZINC001468298591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468298591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001468298591 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C3CC(=O)NC(=O)C3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 11, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 12, 12, 36, 36, 36, 36, 36, 36, 36, 12, 6, 6, 6, 6, 6, 6, 2, 12, 12, 12, 36, 36, 36, 36, 36, 36, 12, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 270) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C3CC(=O)NC(=O)C3)c2)cn1) `ZINC001468298591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468298591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001468298591 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C3CC(=O)NC(=O)C3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 11, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 12, 2, 12, 12, 35, 35, 35, 35, 35, 35, 35, 12, 6, 6, 6, 6, 6, 6, 2, 12, 12, 8, 35, 35, 35, 35, 35, 35, 12, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468298591 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468298591 Building ZINC001468476771 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468476771 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/271 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1cnn(C)c1)c1ncon1) `ZINC001468476771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468476771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468476771 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 25, 25, 25, 25, 25, 7, 21, 21, 21, 21, 2, 2, 2, 2, 2, 2, 2, 4, 25, 25, 25, 25, 25, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/272 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/272' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1cnn(C)c1)c1ncon1) `ZINC001468476771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468476771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468476771 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 25, 25, 25, 25, 25, 7, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 4, 25, 25, 25, 25, 25, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468476771 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771 Building ZINC001468476771 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468476771 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 271) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](c1cnn(C)c1)c1ncon1) `ZINC001468476771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468476771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468476771 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 25, 25, 25, 25, 25, 7, 21, 21, 21, 21, 2, 2, 2, 2, 2, 2, 2, 4, 25, 25, 25, 25, 25, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 272) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](c1cnn(C)c1)c1ncon1) `ZINC001468476771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468476771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468476771 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 25, 25, 25, 25, 25, 7, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 4, 25, 25, 25, 25, 25, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468476771 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476771 Building ZINC001468476773 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468476773 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/273 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1cnn(C)c1)c1ncon1) `ZINC001468476773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468476773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468476773 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 26, 26, 26, 26, 26, 7, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 4, 26, 26, 26, 26, 26, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/274 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1cnn(C)c1)c1ncon1) `ZINC001468476773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468476773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468476773 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 25, 25, 25, 25, 25, 7, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 4, 25, 25, 25, 25, 25, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468476773 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773 Building ZINC001468476773 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468476773 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 273) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](c1cnn(C)c1)c1ncon1) `ZINC001468476773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468476773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468476773 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 26, 26, 26, 26, 26, 7, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 4, 26, 26, 26, 26, 26, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 274) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/274: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](c1cnn(C)c1)c1ncon1) `ZINC001468476773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468476773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468476773 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 25, 25, 25, 25, 25, 7, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 4, 25, 25, 25, 25, 25, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468476773 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468476773 Building ZINC001468533770 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468533770 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/275 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C3CC(=O)NC(=O)C3)cc2)cn1) `ZINC001468533770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468533770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001468533770 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C3CC(=O)NC(=O)C3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 11, 5, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 2, 2, 2, 6, 6, 4, 9, 38, 38, 38, 38, 38, 38, 38, 6, 6, 9, 9, 9, 9, 9, 9, 2, 6, 6, 38, 38, 38, 38, 38, 38, 6, 6, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/276 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/276' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C3CC(=O)NC(=O)C3)cc2)cn1) `ZINC001468533770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468533770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001468533770 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C3CC(=O)NC(=O)C3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 11, 5, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 10, 40, 40, 40, 40, 40, 40, 40, 7, 7, 9, 9, 9, 9, 9, 9, 3, 7, 7, 40, 40, 40, 40, 40, 40, 7, 7, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468533770 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770 Building ZINC001468533770 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468533770 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 275) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C3CC(=O)NC(=O)C3)cc2)cn1) `ZINC001468533770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468533770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001468533770 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C3CC(=O)NC(=O)C3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 11, 5, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 2, 2, 2, 6, 6, 4, 9, 38, 38, 38, 38, 38, 38, 38, 6, 6, 9, 9, 9, 9, 9, 9, 2, 6, 6, 38, 38, 38, 38, 38, 38, 6, 6, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 276) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C3CC(=O)NC(=O)C3)cc2)cn1) `ZINC001468533770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468533770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001468533770 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C3CC(=O)NC(=O)C3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 11, 5, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 7, 7, 5, 10, 40, 40, 40, 40, 40, 40, 40, 7, 7, 9, 9, 9, 9, 9, 9, 3, 7, 7, 40, 40, 40, 40, 40, 40, 7, 7, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468533770 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468533770 Building ZINC001468768872 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468768872 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/277 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCC(=O)Nc2ncc[nH]2)cn1) `ZINC001468768872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468768872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001468768872 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCC(=O)Nc2ncc[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', '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, 5, 5, 1, 11, 8, 1, 8, 1, 1, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 12, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 8, 8, 12, 12, 33, 33, 33, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/278 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCC(=O)Nc2ncc[nH]2)cn1) `ZINC001468768872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468768872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001468768872 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCC(=O)Nc2ncc[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', '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, 5, 5, 1, 11, 8, 1, 8, 1, 1, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 9, 9, 13, 13, 33, 33, 33, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468768872 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872 Building ZINC001468768872 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468768872 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 277) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCC(=O)Nc2ncc[nH]2)cn1) `ZINC001468768872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468768872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001468768872 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCC(=O)Nc2ncc[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', '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, 5, 5, 1, 11, 8, 1, 8, 1, 1, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 12, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 8, 8, 12, 12, 33, 33, 33, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 278) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCC(=O)Nc2ncc[nH]2)cn1) `ZINC001468768872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468768872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001468768872 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCC(=O)Nc2ncc[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', '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, 5, 5, 1, 11, 8, 1, 8, 1, 1, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 9, 9, 13, 13, 33, 33, 33, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468768872 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468768872 Building ZINC001468834966 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468834966 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/279 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC1(N2CCOCC2)CCOCC1) `ZINC001468834966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468834966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001468834966 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC1(N2CCOCC2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 28, 40, 44, 44, 44, 44, 44, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 4, 21, 21, 44, 44, 44, 44, 44, 44, 44, 44, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/280 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC1(N2CCOCC2)CCOCC1) `ZINC001468834966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468834966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001468834966 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC1(N2CCOCC2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 25, 40, 42, 42, 42, 42, 42, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 4, 19, 19, 42, 42, 42, 42, 42, 42, 42, 42, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 133 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468834966 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966 Building ZINC001468834966 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468834966 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 279) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC1(N2CCOCC2)CCOCC1) `ZINC001468834966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468834966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001468834966 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC1(N2CCOCC2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 28, 40, 44, 44, 44, 44, 44, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 4, 21, 21, 44, 44, 44, 44, 44, 44, 44, 44, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 280) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCC1(N2CCOCC2)CCOCC1) `ZINC001468834966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468834966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001468834966 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC1(N2CCOCC2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 25, 40, 42, 42, 42, 42, 42, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 4, 19, 19, 42, 42, 42, 42, 42, 42, 42, 42, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 133 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468834966 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468834966 Building ZINC001468849842 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468849842 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/281 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3COCC[C@@H]32)cc1) `ZINC001468849842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468849842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849842 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3COCC[C@@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 3, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5] 18 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/282 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/282' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3COCC[C@@H]32)cc1) `ZINC001468849842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468849842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849842 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3COCC[C@@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 3, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5] 16 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468849842 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842 Building ZINC001468849842 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468849842 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 281) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCS(=O)(=O)[C@H]3COCC[C@@H]32)cc1) `ZINC001468849842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468849842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849842 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3COCC[C@@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 3, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5] 18 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 282) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/282: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCS(=O)(=O)[C@H]3COCC[C@@H]32)cc1) `ZINC001468849842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468849842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849842 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3COCC[C@@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 3, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5] 16 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468849842 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849842 Building ZINC001468849852 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468849852 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/283 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3COCC[C@H]32)cc1) `ZINC001468849852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468849852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849852 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3COCC[C@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4] 20 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/284 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/284' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3COCC[C@H]32)cc1) `ZINC001468849852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468849852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849852 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3COCC[C@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4] 22 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468849852 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852 Building ZINC001468849852 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468849852 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 283) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/283: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCS(=O)(=O)[C@H]3COCC[C@H]32)cc1) `ZINC001468849852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468849852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849852 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3COCC[C@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4] 20 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 284) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCS(=O)(=O)[C@H]3COCC[C@H]32)cc1) `ZINC001468849852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468849852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849852 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3COCC[C@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4] 22 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468849852 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849852 Building ZINC001468849855 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468849855 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/285 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3COCC[C@@H]32)cc1) `ZINC001468849855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468849855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849855 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3COCC[C@@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4] 24 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/286 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/286' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3COCC[C@@H]32)cc1) `ZINC001468849855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468849855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849855 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3COCC[C@@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 10, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4] 21 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468849855 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855 Building ZINC001468849855 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468849855 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 285) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCS(=O)(=O)[C@@H]3COCC[C@@H]32)cc1) `ZINC001468849855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468849855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849855 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3COCC[C@@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 9, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4] 24 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 286) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCS(=O)(=O)[C@@H]3COCC[C@@H]32)cc1) `ZINC001468849855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468849855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849855 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3COCC[C@@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 10, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4] 21 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468849855 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849855 Building ZINC001468849858 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468849858 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/287 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3COCC[C@H]32)cc1) `ZINC001468849858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468849858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849858 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3COCC[C@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 3, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4] 15 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/288 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/288' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3COCC[C@H]32)cc1) `ZINC001468849858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468849858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849858 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3COCC[C@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 4, 1, 1, 1, 3, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4] 15 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468849858 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858 Building ZINC001468849858 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468849858 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 287) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCS(=O)(=O)[C@@H]3COCC[C@H]32)cc1) `ZINC001468849858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468849858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849858 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3COCC[C@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 3, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4] 15 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 288) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/288: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCS(=O)(=O)[C@@H]3COCC[C@H]32)cc1) `ZINC001468849858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468849858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001468849858 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3COCC[C@H]32)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', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 14, 11, 11, 5, 7, 5, 12, 5, 5, 5, 7, 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, 3, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 4, 1, 1, 1, 3, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4] 15 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001468849858 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001468849858 Building ZINC001469052759 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469052759 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/289 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCC3)S(=O)(=O)CC2)cn1) `ZINC001469052759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469052759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001469052759 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCC3)S(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 15, 24, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/290 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCC3)S(=O)(=O)CC2)cn1) `ZINC001469052759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469052759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001469052759 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCC3)S(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 14, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469052759 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759 Building ZINC001469052759 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469052759 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 289) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/289: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCC3)S(=O)(=O)CC2)cn1) `ZINC001469052759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469052759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001469052759 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CCC3)S(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 15, 24, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 290) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCC3)S(=O)(=O)CC2)cn1) `ZINC001469052759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469052759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001469052759 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CCC3)S(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 14, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469052759 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469052759 Building ZINC001469096250 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469096250 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/291 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001469096250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469096250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001469096250 none NC(=O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 21, 30, 13, 13, 13, 13, 13, 13, 13, 10, 2, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 21, 21, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7] 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]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/292 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001469096250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469096250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001469096250 none NC(=O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 9, 9, 9, 9, 9, 9, 9, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 21, 21, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469096250 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250 Building ZINC001469096250 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469096250 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 291) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001469096250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469096250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001469096250 none NC(=O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 21, 30, 13, 13, 13, 13, 13, 13, 13, 10, 2, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 21, 21, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7] 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]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 292) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001469096250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469096250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001469096250 none NC(=O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 9, 9, 9, 9, 9, 9, 9, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 21, 21, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469096250 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096250 Building ZINC001469096251 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469096251 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/293 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001469096251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469096251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001469096251 none NC(=O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 9, 9, 9, 9, 9, 9, 9, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 21, 21, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/294 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/294' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001469096251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469096251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001469096251 none NC(=O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 32, 14, 14, 14, 14, 14, 14, 14, 11, 2, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 32, 32, 22, 22, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7] 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]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469096251 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251 Building ZINC001469096251 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469096251 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 293) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001469096251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469096251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001469096251 none NC(=O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 9, 9, 9, 9, 9, 9, 9, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 21, 21, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 294) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001469096251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469096251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001469096251 none NC(=O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 32, 14, 14, 14, 14, 14, 14, 14, 11, 2, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 32, 32, 22, 22, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7] 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]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469096251 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469096251 Building ZINC001469294052 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469294052 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/295 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2n[nH]c3cc(C)n(C)c(=O)c32)cn1) `ZINC001469294052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469294052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001469294052 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2n[nH]c3cc(C)n(C)c(=O)c32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 21, 21, 21, 21, 21, 10, 4, 13, 13, 13, 13, 13, 13, 13, 10] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/296 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2n[nH]c3cc(C)n(C)c(=O)c32)cn1) `ZINC001469294052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469294052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001469294052 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2n[nH]c3cc(C)n(C)c(=O)c32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 22, 22, 22, 22, 22, 10, 4, 13, 13, 13, 13, 13, 13, 13, 10] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 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/83982/xcb-8058097.54/working/building/ZINC001469294052 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469294052 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052 Building ZINC001469294052 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469294052 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 295) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2n[nH]c3cc(C)n(C)c(=O)c32)cn1) `ZINC001469294052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469294052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001469294052 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2n[nH]c3cc(C)n(C)c(=O)c32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 21, 21, 21, 21, 21, 10, 4, 13, 13, 13, 13, 13, 13, 13, 10] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 296) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2n[nH]c3cc(C)n(C)c(=O)c32)cn1) `ZINC001469294052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469294052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001469294052 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2n[nH]c3cc(C)n(C)c(=O)c32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 22, 22, 22, 22, 22, 10, 4, 13, 13, 13, 13, 13, 13, 13, 10] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 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/83982/xcb-8058097.54/working/building/ZINC001469294052 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469294052 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469294052 Building ZINC001469387838 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469387838 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/297 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)N1CCOCC1) `ZINC001469387838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469387838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001469387838 none CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 15, 4, 15, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 35, 35, 47, 47, 47, 47, 47, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 8, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 193 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/298 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/298' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)N1CCOCC1) `ZINC001469387838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469387838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001469387838 none CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 25, 25, 15, 4, 15, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 36, 37, 47, 47, 47, 47, 47, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 3, 3, 6, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469387838 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838 Building ZINC001469387838 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469387838 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 297) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)N1CCOCC1) `ZINC001469387838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469387838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001469387838 none CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 15, 4, 15, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 35, 35, 47, 47, 47, 47, 47, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 8, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 193 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 298) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)N1CCOCC1) `ZINC001469387838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469387838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001469387838 none CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 25, 25, 15, 4, 15, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 36, 37, 47, 47, 47, 47, 47, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 3, 3, 6, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469387838 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469387838 Building ZINC001469557647 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469557647 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/299 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)C(F)(F)F)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001469557647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469557647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001469557647 none C[C@H]1[C@@H](NC(=O)C(F)(F)F)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 18, 18, 18, 13, 2, 15, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 28, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/300 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/300' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)C(F)(F)F)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001469557647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469557647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001469557647 none C[C@H]1[C@@H](NC(=O)C(F)(F)F)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 14, 14, 14, 10, 2, 11, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 25, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469557647 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647 Building ZINC001469557647 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469557647 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 299) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)C(F)(F)F)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001469557647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469557647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001469557647 none C[C@H]1[C@@H](NC(=O)C(F)(F)F)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 18, 18, 18, 13, 2, 15, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 28, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 300) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)C(F)(F)F)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001469557647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469557647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001469557647 none C[C@H]1[C@@H](NC(=O)C(F)(F)F)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 14, 14, 14, 10, 2, 11, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 25, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469557647 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469557647 Building ZINC001469574735 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469574735 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/301 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(C2CC2)[nH]1) `ZINC001469574735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469574735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001469574735 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(C2CC2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 13, 13, 4, 4, 5, 5, 5, 5, 17, 17, 5, 4, 4, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/302 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/302' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ncc(C2CC2)[nH]1) `ZINC001469574735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469574735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001469574735 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ncc(C2CC2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 18, 18, 18, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 12, 4, 4, 6, 6, 6, 6, 18, 18, 6, 4, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469574735 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735 Building ZINC001469574735 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469574735 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 301) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(C2CC2)[nH]1) `ZINC001469574735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469574735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001469574735 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(C2CC2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 13, 13, 4, 4, 5, 5, 5, 5, 17, 17, 5, 4, 4, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 302) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ncc(C2CC2)[nH]1) `ZINC001469574735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469574735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001469574735 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ncc(C2CC2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 18, 18, 18, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 12, 4, 4, 6, 6, 6, 6, 18, 18, 6, 4, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469574735 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469574735 Building ZINC001469715477 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469715477 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/303 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2cc(O)nc(O)n2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001469715477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469715477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001469715477 none O=C(N1CC[C@H](c2cc(O)nc(O)n2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 12, 8, 1, 12, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 4, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 400 conformations in input total number of sets (complete confs): 400 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 5, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 16, 16, 50, 100, 100, 16, 16, 2, 2, 4, 2, 2] 400 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: 279 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/304 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/304' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2cc(O)nc(O)n2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001469715477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469715477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001469715477 none O=C(N1CC[C@H](c2cc(O)nc(O)n2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 12, 8, 1, 12, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 4, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 400 conformations in input total number of sets (complete confs): 400 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 6, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 18, 50, 100, 100, 18, 18, 2, 2, 4, 2, 2] 400 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: 280 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469715477 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477 Building ZINC001469715477 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469715477 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 303) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c2cc(O)nc(O)n2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001469715477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469715477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001469715477 none O=C(N1CC[C@H](c2cc(O)nc(O)n2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 12, 8, 1, 12, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 4, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 400 conformations in input total number of sets (complete confs): 400 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 5, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 16, 16, 50, 100, 100, 16, 16, 2, 2, 4, 2, 2] 400 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: 279 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 304) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c2cc(O)nc(O)n2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001469715477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469715477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001469715477 none O=C(N1CC[C@H](c2cc(O)nc(O)n2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 12, 8, 1, 12, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 4, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 400 conformations in input total number of sets (complete confs): 400 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 6, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 18, 50, 100, 100, 18, 18, 2, 2, 4, 2, 2] 400 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: 280 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469715477 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715477 Building ZINC001469715479 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469715479 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/305 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2cc(O)nc(O)n2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001469715479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469715479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001469715479 none O=C(N1CC[C@@H](c2cc(O)nc(O)n2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 12, 8, 1, 12, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 4, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 400 conformations in input total number of sets (complete confs): 400 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 6, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 17, 17, 17, 50, 100, 100, 17, 17, 2, 2, 4, 2, 2] 400 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: 279 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/306 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/306' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2cc(O)nc(O)n2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001469715479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469715479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001469715479 none O=C(N1CC[C@@H](c2cc(O)nc(O)n2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 12, 8, 1, 12, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 4, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 400 conformations in input total number of sets (complete confs): 400 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 18, 50, 100, 100, 18, 18, 2, 2, 4, 2, 2] 400 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: 281 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469715479 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479 Building ZINC001469715479 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469715479 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 305) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c2cc(O)nc(O)n2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001469715479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469715479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001469715479 none O=C(N1CC[C@@H](c2cc(O)nc(O)n2)C1)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 12, 8, 1, 12, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 4, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 400 conformations in input total number of sets (complete confs): 400 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 6, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 17, 17, 17, 50, 100, 100, 17, 17, 2, 2, 4, 2, 2] 400 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: 279 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 306) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c2cc(O)nc(O)n2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001469715479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469715479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001469715479 none O=C(N1CC[C@@H](c2cc(O)nc(O)n2)C1)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 12, 8, 1, 12, 8, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 3, 7, 4, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 400 conformations in input total number of sets (complete confs): 400 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 18, 50, 100, 100, 18, 18, 2, 2, 4, 2, 2] 400 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: 281 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469715479 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469715479 Building ZINC001469813218 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469813218 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/307 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3COC(=O)N[C@@H]3C2)cn1) `ZINC001469813218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469813218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001469813218 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3COC(=O)N[C@@H]3C2)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', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 2, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/308 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/308' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3COC(=O)N[C@@H]3C2)cn1) `ZINC001469813218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469813218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001469813218 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3COC(=O)N[C@@H]3C2)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', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 2, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469813218 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218 Building ZINC001469813218 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469813218 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 307) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3COC(=O)N[C@@H]3C2)cn1) `ZINC001469813218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469813218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001469813218 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3COC(=O)N[C@@H]3C2)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', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 2, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 308) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3COC(=O)N[C@@H]3C2)cn1) `ZINC001469813218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469813218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001469813218 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3COC(=O)N[C@@H]3C2)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', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 2, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001469813218 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001469813218 Building ZINC001470031007 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470031007 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/309 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCS(=O)(=O)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001470031007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470031007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001470031007 none O=C(NCCS(=O)(=O)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 12, 12, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 10, 10, 10, 10, 5, 5, 10, 5, 5] 28 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/310 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/310' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCS(=O)(=O)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001470031007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470031007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001470031007 none O=C(NCCS(=O)(=O)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 13, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 11, 11, 11, 11, 4, 4, 8, 4, 4] 26 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001470031007 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007 Building ZINC001470031007 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470031007 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 309) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCS(=O)(=O)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001470031007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470031007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001470031007 none O=C(NCCS(=O)(=O)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 12, 12, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 10, 10, 10, 10, 5, 5, 10, 5, 5] 28 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 310) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCS(=O)(=O)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001470031007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470031007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001470031007 none O=C(NCCS(=O)(=O)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 13, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 11, 11, 11, 11, 4, 4, 8, 4, 4] 26 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001470031007 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470031007 Building ZINC001470580884 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470580884 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/311 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC[C@@H]1C=NNC1=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001470580884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470580884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001470580884 none O=C(NCCC[C@@H]1C=NNC1=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 17, 22, 31, 31, 31, 31, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 19, 19, 22, 22, 31, 31, 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, 41]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/312 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/312' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC[C@@H]1C=NNC1=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001470580884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470580884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001470580884 none O=C(NCCC[C@@H]1C=NNC1=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 15, 20, 27, 32, 32, 32, 32, 32, 32, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 24, 24, 27, 26, 32, 32, 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, 41]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001470580884 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884 Building ZINC001470580884 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470580884 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 311) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC[C@@H]1C=NNC1=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001470580884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470580884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001470580884 none O=C(NCCC[C@@H]1C=NNC1=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 17, 22, 31, 31, 31, 31, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 19, 19, 22, 22, 31, 31, 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, 41]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 312) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC[C@@H]1C=NNC1=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001470580884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470580884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001470580884 none O=C(NCCC[C@@H]1C=NNC1=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 15, 20, 27, 32, 32, 32, 32, 32, 32, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 24, 24, 27, 26, 32, 32, 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, 41]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001470580884 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580884 Building ZINC001470580887 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470580887 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/313 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC[C@H]1C=NNC1=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001470580887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470580887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001470580887 none O=C(NCCC[C@H]1C=NNC1=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 15, 19, 26, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 23, 23, 25, 26, 33, 33, 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, 41]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/314 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/314' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC[C@H]1C=NNC1=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001470580887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470580887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001470580887 none O=C(NCCC[C@H]1C=NNC1=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 17, 22, 31, 31, 31, 31, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 19, 19, 22, 22, 31, 31, 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, 41]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001470580887 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887 Building ZINC001470580887 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470580887 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 313) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC[C@H]1C=NNC1=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001470580887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470580887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001470580887 none O=C(NCCC[C@H]1C=NNC1=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 15, 19, 26, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 23, 23, 25, 26, 33, 33, 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, 41]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 314) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC[C@H]1C=NNC1=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001470580887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470580887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001470580887 none O=C(NCCC[C@H]1C=NNC1=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 17, 22, 31, 31, 31, 31, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 19, 19, 22, 22, 31, 31, 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, 41]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001470580887 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001470580887 Building ZINC001496028129 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001496028129 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/315 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNCc1nc(N(C)C)no1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001496028129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001496028129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001496028129 none C[C@H](CNCc1nc(N(C)C)no1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 1, 8, 1, 8, 5, 5, 8, 12, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 13, 17, 33, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 17, 33, 33, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/316 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNCc1nc(N(C)C)no1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001496028129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001496028129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001496028129 none C[C@H](CNCc1nc(N(C)C)no1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 1, 8, 1, 8, 5, 5, 8, 12, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 9, 13, 30, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 13, 30, 30, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001496028129 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129 Building ZINC001496028129 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001496028129 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 315) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CNCc1nc(N(C)C)no1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001496028129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001496028129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001496028129 none C[C@H](CNCc1nc(N(C)C)no1)N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 1, 8, 1, 8, 5, 5, 8, 12, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 13, 17, 33, 50, 50, 50, 50, 50, 50, 50, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 17, 33, 33, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 316) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CNCc1nc(N(C)C)no1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001496028129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001496028129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001496028129 none C[C@H](CNCc1nc(N(C)C)no1)N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 1, 8, 1, 8, 5, 5, 8, 12, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 9, 13, 30, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 13, 30, 30, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001496028129 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496028129 Building ZINC001471167515 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471167515 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/317 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCSC1) `ZINC001471167515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471167515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471167515 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 15, 26, 25, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 1, 2, 15, 15, 19, 19, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 23, 24, 25, 26, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/318 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCSC1) `ZINC001471167515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471167515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471167515 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 13, 25, 28, 28, 28, 28, 28, 1, 1, 1, 1, 4, 4, 1, 2, 13, 13, 20, 20, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 23, 24, 25, 26, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471167515 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515 Building ZINC001471167515 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471167515 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 317) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCSC1) `ZINC001471167515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471167515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471167515 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 15, 26, 25, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 1, 2, 15, 15, 19, 19, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 23, 24, 25, 26, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 318) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCSC1) `ZINC001471167515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471167515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471167515 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 13, 25, 28, 28, 28, 28, 28, 1, 1, 1, 1, 4, 4, 1, 2, 13, 13, 20, 20, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 23, 24, 25, 26, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471167515 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167515 Building ZINC001471167516 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471167516 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/319 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCSC1) `ZINC001471167516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471167516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471167516 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 14, 26, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 14, 14, 19, 19, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 23, 24, 25, 26, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/320 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCSC1) `ZINC001471167516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471167516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471167516 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 14, 25, 28, 28, 28, 28, 28, 1, 1, 1, 1, 4, 4, 1, 2, 14, 14, 18, 18, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 23, 24, 25, 26, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471167516 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516 Building ZINC001471167516 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471167516 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 319) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCSC1) `ZINC001471167516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471167516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471167516 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 14, 26, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 1, 2, 14, 14, 19, 19, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 23, 24, 25, 26, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 320) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCSC1) `ZINC001471167516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471167516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471167516 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.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, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 14, 25, 28, 28, 28, 28, 28, 1, 1, 1, 1, 4, 4, 1, 2, 14, 14, 18, 18, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 23, 24, 25, 26, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471167516 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471167516 Building ZINC001471292750 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471292750 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/321 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[C@@H](O)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001471292750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471292750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471292750 none COC(=O)[C@H]1C[C@@H](O)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 9, 17, 9, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 17, 17, 17, 9, 9, 27, 9, 9, 6, 10, 10, 6, 10, 10, 6] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/322 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[C@@H](O)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001471292750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471292750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471292750 none COC(=O)[C@H]1C[C@@H](O)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 10, 23, 10, 10, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 13, 13, 6, 23, 23, 23, 10, 10, 30, 10, 10, 6, 13, 13, 13, 13, 13, 6] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471292750 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750 Building ZINC001471292750 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471292750 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 321) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[C@@H](O)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001471292750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471292750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471292750 none COC(=O)[C@H]1C[C@@H](O)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 9, 17, 9, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 17, 17, 17, 9, 9, 27, 9, 9, 6, 10, 10, 6, 10, 10, 6] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 322) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1C[C@@H](O)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001471292750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471292750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471292750 none COC(=O)[C@H]1C[C@@H](O)CN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 10, 23, 10, 10, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 13, 13, 6, 23, 23, 23, 10, 10, 30, 10, 10, 6, 13, 13, 13, 13, 13, 6] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471292750 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471292750 Building ZINC001471343833 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471343833 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/323 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CO)Cc1cnc[nH]1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471343833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471343833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471343833 none O=C(N[C@H](CO)Cc1cnc[nH]1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 1, 1, 8, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 19, 12, 19, 23, 23, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 19, 19, 57, 19, 19, 23, 23, 6, 6, 6, 6] 150 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: 191 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/324 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/324' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CO)Cc1cnc[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471343833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471343833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471343833 none O=C(N[C@H](CO)Cc1cnc[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 1, 1, 8, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 28, 16, 23, 29, 29, 29, 29, 29, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 84, 23, 23, 29, 29, 5, 5, 5, 5] 150 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: 253 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471343833 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833 Building ZINC001471343833 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471343833 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 323) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](CO)Cc1cnc[nH]1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471343833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471343833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471343833 none O=C(N[C@H](CO)Cc1cnc[nH]1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 1, 1, 8, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 12, 12, 19, 12, 19, 23, 23, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 19, 19, 57, 19, 19, 23, 23, 6, 6, 6, 6] 150 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: 191 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 324) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](CO)Cc1cnc[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471343833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471343833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471343833 none O=C(N[C@H](CO)Cc1cnc[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 1, 1, 8, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 28, 16, 23, 29, 29, 29, 29, 29, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 84, 23, 23, 29, 29, 5, 5, 5, 5] 150 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: 253 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471343833 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471343833 Building ZINC001471389571 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471389571 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/325 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C[C@@H](O)CNC2=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471389571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471389571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001471389571 none O=C(N1CCC2(CC1)C[C@@H](O)CNC2=O)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', '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, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 31, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 144, 48, 48, 48, 4, 4, 8, 4, 4] 300 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, 40, 41, 42, 43]) total number of confs: 232 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/326 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C[C@@H](O)CNC2=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471389571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471389571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001471389571 none O=C(N1CCC2(CC1)C[C@@H](O)CNC2=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', '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, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [12, 2, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 147, 49, 49, 49, 4, 4, 8, 4, 4] 300 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]) total number of confs: 238 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471389571 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571 Building ZINC001471389571 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471389571 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 325) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C[C@@H](O)CNC2=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471389571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471389571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001471389571 none O=C(N1CCC2(CC1)C[C@@H](O)CNC2=O)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', '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, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 31, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 144, 48, 48, 48, 4, 4, 8, 4, 4] 300 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, 40, 41, 42, 43]) total number of confs: 232 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 326) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C[C@@H](O)CNC2=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471389571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471389571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001471389571 none O=C(N1CCC2(CC1)C[C@@H](O)CNC2=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', '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, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [12, 2, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 147, 49, 49, 49, 4, 4, 8, 4, 4] 300 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]) total number of confs: 238 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471389571 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389571 Building ZINC001471389572 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471389572 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/327 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C[C@H](O)CNC2=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471389572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471389572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001471389572 none O=C(N1CCC2(CC1)C[C@H](O)CNC2=O)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', '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, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 150, 50, 50, 50, 2, 2, 4, 2, 2] 300 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, 40, 41, 42, 43]) total number of confs: 233 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/328 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/328' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C[C@H](O)CNC2=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471389572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471389572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001471389572 none O=C(N1CCC2(CC1)C[C@H](O)CNC2=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', '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, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 150, 50, 50, 50, 3, 3, 6, 3, 3] 300 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, 40, 41, 42, 43]) total number of confs: 240 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471389572 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572 Building ZINC001471389572 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471389572 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 327) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C[C@H](O)CNC2=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471389572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471389572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001471389572 none O=C(N1CCC2(CC1)C[C@H](O)CNC2=O)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', '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, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 150, 50, 50, 50, 2, 2, 4, 2, 2] 300 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, 40, 41, 42, 43]) total number of confs: 233 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 328) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)C[C@H](O)CNC2=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471389572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471389572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001471389572 none O=C(N1CCC2(CC1)C[C@H](O)CNC2=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', '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, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 150, 50, 50, 50, 3, 3, 6, 3, 3] 300 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, 40, 41, 42, 43]) total number of confs: 240 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471389572 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471389572 Building ZINC001471467867 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471467867 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/329 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(O)nc1=O) `ZINC001471467867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471467867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471467867 none COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 27, 27, 27, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 38, 38, 27, 11, 11, 2, 2, 2, 2, 2, 81] 150 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]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/330 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(O)nc1=O) `ZINC001471467867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471467867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471467867 none COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 27, 27, 27, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 39, 39, 27, 11, 11, 2, 2, 2, 2, 2, 81] 150 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]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471467867 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867 Building ZINC001471467867 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471467867 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 329) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(O)nc1=O) `ZINC001471467867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471467867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471467867 none COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 27, 27, 27, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 38, 38, 27, 11, 11, 2, 2, 2, 2, 2, 81] 150 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]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 330) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(O)nc1=O) `ZINC001471467867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471467867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471467867 none COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 27, 27, 27, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 39, 39, 27, 11, 11, 2, 2, 2, 2, 2, 81] 150 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]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471467867 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471467867 Building ZINC001471623282 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471623282 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/331 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cccn1C)Oc1ccccc1) `ZINC001471623282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471623282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001471623282 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cccn1C)Oc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 28, 11, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 25, 29, 29, 25, 29, 29, 28, 28, 28, 11, 11, 2, 3, 3, 3, 3, 3, 3, 29, 29, 25, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/332 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cccn1C)Oc1ccccc1) `ZINC001471623282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471623282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001471623282 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cccn1C)Oc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 27, 11, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 14, 26, 31, 31, 26, 31, 31, 27, 27, 27, 11, 11, 3, 3, 3, 3, 3, 3, 3, 31, 31, 26, 31, 31] 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471623282 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282 Building ZINC001471623282 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471623282 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 331) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cccn1C)Oc1ccccc1) `ZINC001471623282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471623282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001471623282 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cccn1C)Oc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 28, 11, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 25, 29, 29, 25, 29, 29, 28, 28, 28, 11, 11, 2, 3, 3, 3, 3, 3, 3, 29, 29, 25, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 332) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cccn1C)Oc1ccccc1) `ZINC001471623282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471623282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001471623282 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cccn1C)Oc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 27, 11, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 14, 26, 31, 31, 26, 31, 31, 27, 27, 27, 11, 11, 3, 3, 3, 3, 3, 3, 3, 31, 31, 26, 31, 31] 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471623282 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471623282 Building ZINC001471641652 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471641652 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/333 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 48, 10] 150 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: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/334 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 21, 10, 10, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 60, 10] 150 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: 196 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/335 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/335' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 48, 10] 150 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: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/336 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/336' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 21, 10, 10, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 60, 10] 150 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: 196 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471641652 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 Building ZINC001471641652 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471641652 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 333) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 48, 10] 150 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: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 334) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 21, 10, 10, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 60, 10] 150 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: 196 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 335) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 48, 10] 150 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: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 336) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 21, 10, 10, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 60, 10] 150 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: 196 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471641652 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 Building ZINC001471641652 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471641652 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 333) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 48, 10] 150 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: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 334) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 21, 10, 10, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 60, 10] 150 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: 196 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 335) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 48, 10] 150 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: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 336) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 21, 10, 10, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 60, 10] 150 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: 196 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471641652 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 Building ZINC001471641652 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471641652 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 333) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 48, 10] 150 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: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 334) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 21, 10, 10, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 60, 10] 150 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: 196 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 335) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 48, 10] 150 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: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 336) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2C[C@@H]3CCCN3C[C@@H]2CO)cn1) `ZINC001471641652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471641652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471641652 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCCN3C[C@@H]2CO)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', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 21, 10, 10, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 60, 10] 150 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: 196 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471641652 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471641652 Building ZINC001471642817 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471642817 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/337 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@]1(O)C(=O)Nc2ccccc21)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471642817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471642817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471642817 none O=C(NCC[C@]1(O)C(=O)Nc2ccccc21)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 24, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 2, 4, 4, 4, 5, 24, 24, 26, 26, 150, 50, 50, 50, 50, 50, 4, 4, 8, 4, 4] 300 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/338 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/338' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@]1(O)C(=O)Nc2ccccc21)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471642817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471642817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471642817 none O=C(NCC[C@]1(O)C(=O)Nc2ccccc21)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 25, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 25, 25, 28, 28, 150, 50, 50, 50, 50, 50, 5, 5, 10, 5, 5] 300 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, 40]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471642817 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817 Building ZINC001471642817 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471642817 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 337) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@]1(O)C(=O)Nc2ccccc21)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471642817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471642817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471642817 none O=C(NCC[C@]1(O)C(=O)Nc2ccccc21)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 24, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 2, 4, 4, 4, 5, 24, 24, 26, 26, 150, 50, 50, 50, 50, 50, 4, 4, 8, 4, 4] 300 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 338) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@]1(O)C(=O)Nc2ccccc21)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471642817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471642817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471642817 none O=C(NCC[C@]1(O)C(=O)Nc2ccccc21)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 25, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 25, 25, 28, 28, 150, 50, 50, 50, 50, 50, 5, 5, 10, 5, 5] 300 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, 40]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471642817 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642817 Building ZINC001471642819 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471642819 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/339 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@]1(O)C(=O)Nc2ccccc21)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471642819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471642819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471642819 none O=C(NCC[C@@]1(O)C(=O)Nc2ccccc21)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 25, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 25, 25, 28, 28, 150, 50, 50, 50, 50, 50, 4, 4, 8, 4, 4] 300 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, 40]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/340 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@]1(O)C(=O)Nc2ccccc21)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471642819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471642819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471642819 none O=C(NCC[C@@]1(O)C(=O)Nc2ccccc21)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 25, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 25, 25, 27, 27, 150, 50, 50, 50, 50, 50, 4, 4, 8, 4, 4] 300 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, 40]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471642819 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819 Building ZINC001471642819 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471642819 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 339) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@]1(O)C(=O)Nc2ccccc21)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471642819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471642819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471642819 none O=C(NCC[C@@]1(O)C(=O)Nc2ccccc21)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 25, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 25, 25, 28, 28, 150, 50, 50, 50, 50, 50, 4, 4, 8, 4, 4] 300 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, 40]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 340) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@]1(O)C(=O)Nc2ccccc21)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471642819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471642819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471642819 none O=C(NCC[C@@]1(O)C(=O)Nc2ccccc21)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 25, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 25, 25, 27, 27, 150, 50, 50, 50, 50, 50, 4, 4, 8, 4, 4] 300 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, 40]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471642819 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471642819 Building ZINC001471655931 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471655931 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/341 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O) `ZINC001471655931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471655931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001471655931 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O 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', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', '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, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 8, 8, 13, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 7, 7, 7, 7, 8, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/342 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O) `ZINC001471655931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471655931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001471655931 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O 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', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', '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, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 8, 8, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 8, 8, 7, 7, 7, 7, 8, 34, 34, 34, 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, 38]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471655931 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931 Building ZINC001471655931 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471655931 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 341) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1Cc2cccnc2NC1=O) `ZINC001471655931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471655931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001471655931 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O 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', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', '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, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 8, 8, 13, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 7, 7, 7, 7, 8, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 342) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1Cc2cccnc2NC1=O) `ZINC001471655931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471655931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001471655931 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2cccnc2NC1=O 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', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', '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, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 8, 8, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 8, 8, 7, 7, 7, 7, 8, 34, 34, 34, 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, 38]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471655931 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655931 Building ZINC001471655932 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471655932 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/343 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O) `ZINC001471655932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471655932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001471655932 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O 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', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', '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, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 8, 8, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 8, 8, 7, 7, 7, 7, 8, 34, 34, 34, 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, 38]) total number of confs: 94 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/344 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O) `ZINC001471655932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471655932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001471655932 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O 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', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', '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, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 7, 7, 7, 7, 9, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471655932 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932 Building ZINC001471655932 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471655932 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 343) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1Cc2cccnc2NC1=O) `ZINC001471655932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471655932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001471655932 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O 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', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', '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, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 8, 8, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 8, 8, 7, 7, 7, 7, 8, 34, 34, 34, 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, 38]) total number of confs: 94 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 344) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1Cc2cccnc2NC1=O) `ZINC001471655932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471655932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001471655932 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1Cc2cccnc2NC1=O 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', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', '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, 8, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 9, 9, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 7, 7, 7, 7, 9, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471655932 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471655932 Building ZINC001471666416 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471666416 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/345 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNS(N)(=O)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001471666416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471666416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001471666416 none CC(C)(CNS(N)(=O)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 8, 11, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 6, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 22, 33, 41, 41, 41, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 22, 22, 33, 41, 41, 4, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/346 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/346' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNS(N)(=O)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001471666416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471666416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001471666416 none CC(C)(CNS(N)(=O)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 8, 11, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 6, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 22, 33, 41, 41, 41, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 22, 22, 33, 41, 41, 4, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471666416 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416 Building ZINC001471666416 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471666416 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 345) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNS(N)(=O)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001471666416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471666416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001471666416 none CC(C)(CNS(N)(=O)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 8, 11, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 6, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 22, 33, 41, 41, 41, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 22, 22, 33, 41, 41, 4, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 346) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNS(N)(=O)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001471666416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471666416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001471666416 none CC(C)(CNS(N)(=O)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 8, 11, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 6, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 22, 33, 41, 41, 41, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 22, 22, 33, 41, 41, 4, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471666416 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666416 Building ZINC001471666707 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471666707 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/347 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNS(N)(=O)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001471666707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471666707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471666707 none CC(C)(CNS(N)(=O)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 8, 11, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 6, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 28, 44, 49, 49, 49, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 12, 12, 28, 28, 44, 49, 49, 4, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/348 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/348' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNS(N)(=O)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001471666707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471666707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471666707 none CC(C)(CNS(N)(=O)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 8, 11, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 6, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 28, 44, 49, 49, 49, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 12, 12, 28, 28, 44, 49, 49, 4, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471666707 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707 Building ZINC001471666707 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471666707 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 347) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNS(N)(=O)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001471666707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471666707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471666707 none CC(C)(CNS(N)(=O)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 8, 11, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 6, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 28, 44, 49, 49, 49, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 12, 12, 28, 28, 44, 49, 49, 4, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 348) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNS(N)(=O)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001471666707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471666707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471666707 none CC(C)(CNS(N)(=O)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 8, 11, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 6, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 28, 44, 49, 49, 49, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 12, 12, 28, 28, 44, 49, 49, 4, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471666707 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471666707 Building ZINC001471762419 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471762419 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/349 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)NCc1ccccc1) `ZINC001471762419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471762419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001471762419 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)NCc1ccccc1 NO_LONG_NAME dock atom 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', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete 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, 4, 4, 4, 8, 11, 11, 11, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 4, 8, 8, 11, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/350 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)NCc1ccccc1) `ZINC001471762419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471762419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001471762419 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)NCc1ccccc1 NO_LONG_NAME dock atom 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', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete 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, 4, 4, 4, 8, 11, 11, 11, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 4, 8, 8, 11, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471762419 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419 Building ZINC001471762419 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471762419 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 349) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)NCc1ccccc1) `ZINC001471762419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471762419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001471762419 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)NCc1ccccc1 NO_LONG_NAME dock atom 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', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete 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, 4, 4, 4, 8, 11, 11, 11, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 4, 8, 8, 11, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 350) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)NCc1ccccc1) `ZINC001471762419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471762419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001471762419 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)NCc1ccccc1 NO_LONG_NAME dock atom 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', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete 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, 4, 4, 4, 8, 11, 11, 11, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 4, 8, 8, 11, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471762419 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471762419 Building ZINC001471764881 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471764881 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/351 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c(O)nc1=O) `ZINC001471764881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471764881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001471764881 none CC(C)(C)n1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 23, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 4, 3, 3, 6, 3, 3, 150] 300 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: 278 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/352 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c(O)nc1=O) `ZINC001471764881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471764881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001471764881 none CC(C)(C)n1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 4, 3, 3, 6, 3, 3, 150] 300 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: 274 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471764881 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881 Building ZINC001471764881 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471764881 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 351) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c(O)nc1=O) `ZINC001471764881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471764881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001471764881 none CC(C)(C)n1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 23, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 4, 3, 3, 6, 3, 3, 150] 300 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: 278 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 352) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c(O)nc1=O) `ZINC001471764881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471764881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001471764881 none CC(C)(C)n1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 4, 3, 3, 6, 3, 3, 150] 300 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: 274 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471764881 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471764881 Building ZINC001471780608 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471780608 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/353 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1c[nH]nc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001471780608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471780608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471780608 none CN(C)C(=O)c1c[nH]nc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 22, 24, 9, 22, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 24, 24, 24, 24, 24, 24, 9, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/354 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/354' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1c[nH]nc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001471780608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471780608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471780608 none CN(C)C(=O)c1c[nH]nc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 27, 9, 25, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 27, 27, 27, 27, 27, 27, 9, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471780608 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608 Building ZINC001471780608 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471780608 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 353) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1c[nH]nc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001471780608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471780608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471780608 none CN(C)C(=O)c1c[nH]nc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 22, 24, 9, 22, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 24, 24, 24, 24, 24, 24, 9, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 354) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1c[nH]nc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001471780608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471780608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471780608 none CN(C)C(=O)c1c[nH]nc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 27, 9, 25, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 27, 27, 27, 27, 27, 27, 9, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471780608 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471780608 Building ZINC001471822275 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471822275 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/355 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(C1)C[C@H](O)CNC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471822275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471822275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471822275 none O=C(N1CC2(C1)C[C@H](O)CNC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 63, 21, 21, 21, 6, 6, 6, 6] 150 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/356 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/356' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(C1)C[C@H](O)CNC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471822275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471822275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471822275 none O=C(N1CC2(C1)C[C@H](O)CNC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 69, 23, 23, 23, 6, 6, 6, 6] 150 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471822275 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275 Building ZINC001471822275 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471822275 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 355) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(C1)C[C@H](O)CNC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471822275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471822275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471822275 none O=C(N1CC2(C1)C[C@H](O)CNC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 63, 21, 21, 21, 6, 6, 6, 6] 150 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 356) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(C1)C[C@H](O)CNC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471822275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471822275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471822275 none O=C(N1CC2(C1)C[C@H](O)CNC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 69, 23, 23, 23, 6, 6, 6, 6] 150 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471822275 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822275 Building ZINC001471822276 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471822276 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/357 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(C1)C[C@@H](O)CNC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471822276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471822276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471822276 none O=C(N1CC2(C1)C[C@@H](O)CNC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 63, 21, 21, 21, 6, 6, 6, 6] 150 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/358 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/358' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(C1)C[C@@H](O)CNC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471822276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471822276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471822276 none O=C(N1CC2(C1)C[C@@H](O)CNC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 5, 19, 19, 18, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 57, 19, 19, 19, 6, 6, 6, 6] 150 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471822276 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276 Building ZINC001471822276 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471822276 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 357) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(C1)C[C@@H](O)CNC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471822276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471822276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471822276 none O=C(N1CC2(C1)C[C@@H](O)CNC2=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 63, 21, 21, 21, 6, 6, 6, 6] 150 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 358) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(C1)C[C@@H](O)CNC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471822276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471822276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471822276 none O=C(N1CC2(C1)C[C@@H](O)CNC2=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 5, 19, 19, 18, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 57, 19, 19, 19, 6, 6, 6, 6] 150 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471822276 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471822276 Building ZINC001471850092 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471850092 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/359 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1nnc2c(=O)[nH]ccn12)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001471850092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471850092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001471850092 none O=C(NCCc1nnc2c(=O)[nH]ccn12)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 25, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 25, 25, 37, 37, 50, 50, 4, 4, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/360 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/360' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1nnc2c(=O)[nH]ccn12)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001471850092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471850092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001471850092 none O=C(NCCc1nnc2c(=O)[nH]ccn12)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 25, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 2, 4, 4, 6, 25, 25, 37, 37, 50, 50, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471850092 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092 Building ZINC001471850092 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471850092 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 359) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1nnc2c(=O)[nH]ccn12)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001471850092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471850092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001471850092 none O=C(NCCc1nnc2c(=O)[nH]ccn12)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 25, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 25, 25, 37, 37, 50, 50, 4, 4, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 360) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1nnc2c(=O)[nH]ccn12)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001471850092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471850092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001471850092 none O=C(NCCc1nnc2c(=O)[nH]ccn12)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 25, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 2, 4, 4, 6, 25, 25, 37, 37, 50, 50, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471850092 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471850092 Building ZINC001471851259 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471851259 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/361 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)[nH]ccn23)c1) `ZINC001471851259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001471851259 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)[nH]ccn23)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', '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, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 8, 8, 1, 1, 1, 1, 5, 5, 5, 17, 23, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 2, 8, 8, 5, 17, 17, 23, 23, 28, 28, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/362 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/362' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)[nH]ccn23)c1) `ZINC001471851259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001471851259 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)[nH]ccn23)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', '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, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 8, 8, 1, 1, 1, 1, 5, 5, 5, 17, 23, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 2, 8, 8, 5, 17, 17, 23, 23, 28, 28, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471851259 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259 Building ZINC001471851259 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471851259 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 361) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)[nH]ccn23)c1) `ZINC001471851259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001471851259 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)[nH]ccn23)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', '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, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 8, 8, 1, 1, 1, 1, 5, 5, 5, 17, 23, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 2, 8, 8, 5, 17, 17, 23, 23, 28, 28, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 362) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)[nH]ccn23)c1) `ZINC001471851259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001471851259 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCc2nnc3c(=O)[nH]ccn23)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'C.2', 'C.2', 'N.pl3', '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, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 11, 8, 6, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 8, 8, 1, 1, 1, 1, 5, 5, 5, 17, 23, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 2, 8, 8, 5, 17, 17, 23, 23, 28, 28, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471851259 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471851259 Building ZINC001471854256 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471854256 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/363 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3nn[nH]n3)C2)cn1) `ZINC001471854256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471854256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001471854256 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3nn[nH]n3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 8, 8, 8, 6, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 2, 5, 8, 9, 9, 9, 9, 9, 9, 22, 29, 29, 29, 29, 29, 9, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 9, 9, 9, 9, 9, 9, 22, 22, 9, 9, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/364 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/364' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3nn[nH]n3)C2)cn1) `ZINC001471854256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471854256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001471854256 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3nn[nH]n3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 8, 8, 8, 6, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 2, 3, 5, 8, 8, 8, 8, 8, 8, 23, 31, 31, 31, 31, 31, 8, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 8, 8, 8, 8, 8, 8, 23, 23, 8, 8, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471854256 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256 Building ZINC001471854256 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471854256 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 363) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3nn[nH]n3)C2)cn1) `ZINC001471854256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471854256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001471854256 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3nn[nH]n3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 8, 8, 8, 6, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 2, 5, 8, 9, 9, 9, 9, 9, 9, 22, 29, 29, 29, 29, 29, 9, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 9, 9, 9, 9, 9, 9, 22, 22, 9, 9, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 364) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3nn[nH]n3)C2)cn1) `ZINC001471854256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471854256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001471854256 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3nn[nH]n3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 8, 8, 8, 6, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 2, 3, 5, 8, 8, 8, 8, 8, 8, 23, 31, 31, 31, 31, 31, 8, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 8, 8, 8, 8, 8, 8, 23, 23, 8, 8, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471854256 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854256 Building ZINC001471854257 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471854257 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/365 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3nn[nH]n3)C2)cn1) `ZINC001471854257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471854257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001471854257 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3nn[nH]n3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 8, 8, 8, 6, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 2, 3, 5, 8, 8, 8, 8, 8, 8, 23, 31, 31, 31, 31, 31, 8, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 8, 8, 8, 8, 8, 8, 23, 23, 8, 8, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/366 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/366' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3nn[nH]n3)C2)cn1) `ZINC001471854257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471854257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001471854257 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3nn[nH]n3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 8, 8, 8, 6, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 16, 16, 6, 6, 1, 1, 1, 2, 4, 7, 8, 8, 8, 8, 8, 8, 19, 31, 31, 31, 31, 31, 8, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 8, 8, 8, 8, 8, 8, 19, 19, 8, 8, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471854257 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257 Building ZINC001471854257 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471854257 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 365) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3nn[nH]n3)C2)cn1) `ZINC001471854257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471854257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001471854257 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3nn[nH]n3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 8, 8, 8, 6, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 2, 3, 5, 8, 8, 8, 8, 8, 8, 23, 31, 31, 31, 31, 31, 8, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 8, 8, 8, 8, 8, 8, 23, 23, 8, 8, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 366) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3nn[nH]n3)C2)cn1) `ZINC001471854257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471854257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001471854257 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3nn[nH]n3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 8, 8, 8, 6, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 16, 16, 6, 6, 1, 1, 1, 2, 4, 7, 8, 8, 8, 8, 8, 8, 19, 31, 31, 31, 31, 31, 8, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 8, 8, 8, 8, 8, 8, 19, 19, 8, 8, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471854257 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471854257 Building ZINC001471862161 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471862161 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/367 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCNC2=O) `ZINC001471862161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471862161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001471862161 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCNC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 25, 36, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 4, 25, 25, 36, 36, 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]) total number of confs: 170 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/368 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/368' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCNC2=O) `ZINC001471862161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471862161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001471862161 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCNC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 34, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 2, 2, 2, 4, 24, 24, 34, 34, 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]) total number of confs: 163 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471862161 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161 Building ZINC001471862161 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471862161 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 367) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCCc1nnc2n1CCNC2=O) `ZINC001471862161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471862161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001471862161 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCNC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 25, 36, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 4, 25, 25, 36, 36, 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]) total number of confs: 170 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 368) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCCc1nnc2n1CCNC2=O) `ZINC001471862161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471862161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001471862161 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCc1nnc2n1CCNC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 24, 34, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 2, 2, 2, 4, 24, 24, 34, 34, 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]) total number of confs: 163 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471862161 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471862161 Building ZINC001471900467 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471900467 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/369 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001471900467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471900467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001471900467 none CN(C)S(=O)(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.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, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 50, 50, 22, 50, 50, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 22, 22, 50, 50, 50, 50, 50, 50, 15, 15, 4, 3, 3, 6, 3, 3, 22, 22, 22, 22] 100 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: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/370 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/370' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001471900467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471900467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001471900467 none CN(C)S(=O)(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.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, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 50, 50, 25, 50, 50, 16, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 25, 25, 50, 50, 50, 50, 50, 50, 16, 16, 4, 4, 4, 8, 4, 4, 25, 25, 25, 25] 100 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: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471900467 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467 Building ZINC001471900467 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471900467 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 369) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)S(=O)(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001471900467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471900467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001471900467 none CN(C)S(=O)(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.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, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 50, 50, 22, 50, 50, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 22, 22, 50, 50, 50, 50, 50, 50, 15, 15, 4, 3, 3, 6, 3, 3, 22, 22, 22, 22] 100 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: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 370) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)S(=O)(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001471900467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471900467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001471900467 none CN(C)S(=O)(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.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, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 50, 50, 25, 50, 50, 16, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 25, 25, 50, 50, 50, 50, 50, 50, 16, 16, 4, 4, 4, 8, 4, 4, 25, 25, 25, 25] 100 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: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471900467 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471900467 Building ZINC001471902438 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471902438 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/371 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cnc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)s1) `ZINC001471902438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471902438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471902438 none COC(=O)c1cnc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 26, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 26, 36, 36, 36, 26, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/372 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/372' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cnc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)s1) `ZINC001471902438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471902438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471902438 none COC(=O)c1cnc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 35, 25, 25, 25, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 35, 35, 35, 25, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471902438 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438 Building ZINC001471902438 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471902438 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 371) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cnc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)s1) `ZINC001471902438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471902438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471902438 none COC(=O)c1cnc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 26, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 26, 36, 36, 36, 26, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 372) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cnc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)s1) `ZINC001471902438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471902438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471902438 none COC(=O)c1cnc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 35, 25, 25, 25, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 35, 35, 35, 25, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471902438 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471902438 Building ZINC001471903629 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471903629 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/373 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1) `ZINC001471903629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471903629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001471903629 none NS(=O)(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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: [8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 35, 48, 48, 26, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 35, 35, 35, 48, 48, 18, 18, 5, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35] 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/374 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1) `ZINC001471903629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471903629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001471903629 none NS(=O)(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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: [8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 48, 48, 25, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 34, 34, 34, 48, 48, 17, 17, 5, 4, 4, 4, 4, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471903629 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629 Building ZINC001471903629 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471903629 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 373) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1) `ZINC001471903629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471903629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001471903629 none NS(=O)(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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: [8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 35, 48, 48, 26, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 35, 35, 35, 48, 48, 18, 18, 5, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35] 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 374) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1) `ZINC001471903629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471903629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001471903629 none NS(=O)(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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: [8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 48, 48, 25, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 34, 34, 34, 48, 48, 17, 17, 5, 4, 4, 4, 4, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471903629 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471903629 Building ZINC001471911450 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471911450 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/375 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(O)nc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)CC2)n1) `ZINC001471911450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471911450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001471911450 none Cc1cc(O)nc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 1, 1, 1, 12, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 7, 1, 11, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 17, 50, 50, 50, 50, 50, 100, 17, 17, 17, 17, 2, 2, 4, 2, 2, 17, 17, 17, 17] 200 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/376 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(O)nc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)CC2)n1) `ZINC001471911450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471911450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001471911450 none Cc1cc(O)nc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 1, 1, 1, 12, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 8, 2, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 100, 20, 20, 20, 20, 3, 3, 6, 3, 3, 20, 20, 20, 20] 200 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471911450 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450 Building ZINC001471911450 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471911450 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 375) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)CC2)n1) `ZINC001471911450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471911450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001471911450 none Cc1cc(O)nc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 1, 1, 1, 12, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 7, 1, 11, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 17, 50, 50, 50, 50, 50, 100, 17, 17, 17, 17, 2, 2, 4, 2, 2, 17, 17, 17, 17] 200 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 376) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/376: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)nc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)CC2)n1) `ZINC001471911450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471911450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001471911450 none Cc1cc(O)nc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 1, 1, 1, 12, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 8, 2, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 100, 20, 20, 20, 20, 3, 3, 6, 3, 3, 20, 20, 20, 20] 200 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471911450 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471911450 Building ZINC001471921517 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471921517 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/377 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC1CCC=CCC1) `ZINC001471921517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471921517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471921517 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC1CCC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 8, 4, 1, 1, 1, 1, 3, 3, 7, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 8, 8, 4, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/378 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/378' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC1CCC=CCC1) `ZINC001471921517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471921517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471921517 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC1CCC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 8, 4, 1, 1, 1, 1, 3, 3, 8, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 8, 8, 4, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471921517 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517 Building ZINC001471921517 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471921517 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 377) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC1CCC=CCC1) `ZINC001471921517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471921517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471921517 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC1CCC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 8, 4, 1, 1, 1, 1, 3, 3, 7, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 8, 8, 4, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 378) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC1CCC=CCC1) `ZINC001471921517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471921517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471921517 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC1CCC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 8, 4, 1, 1, 1, 1, 3, 3, 8, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 8, 8, 4, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471921517 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471921517 Building ZINC001471934509 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471934509 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/379 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1[C@@H]1C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471934509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471934509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471934509 none C[C@@H]1C[C@H]1[C@@H]1C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 11, 20, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 4, 4, 4, 9, 9, 9, 4, 4, 4, 20, 20, 20, 20, 20, 11, 11, 3, 4, 9, 9, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/380 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1[C@@H]1C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471934509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471934509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471934509 none C[C@@H]1C[C@H]1[C@@H]1C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 10, 18, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 4, 4, 4, 9, 9, 9, 4, 4, 4, 18, 18, 18, 18, 18, 10, 10, 3, 4, 9, 9, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471934509 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509 Building ZINC001471934509 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471934509 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 379) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1[C@@H]1C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471934509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471934509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471934509 none C[C@@H]1C[C@H]1[C@@H]1C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 11, 20, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 4, 4, 4, 9, 9, 9, 4, 4, 4, 20, 20, 20, 20, 20, 11, 11, 3, 4, 9, 9, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 380) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1[C@@H]1C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471934509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471934509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471934509 none C[C@@H]1C[C@H]1[C@@H]1C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 10, 18, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 4, 4, 4, 9, 9, 9, 4, 4, 4, 18, 18, 18, 18, 18, 10, 10, 3, 4, 9, 9, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471934509 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471934509 Building ZINC001471977975 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471977975 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/381 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 42, 49, 21, 21, 21, 21, 21, 7, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 42, 42, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/382 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/382' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 42, 49, 21, 21, 21, 21, 21, 7, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 42, 42, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/383 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/383' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 40, 49, 21, 21, 21, 21, 21, 9, 1, 10, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 40, 40, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/384 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/384' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 40, 49, 21, 21, 21, 21, 21, 9, 1, 10, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 40, 40, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471977975 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 Building ZINC001471977975 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471977975 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 381) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 42, 49, 21, 21, 21, 21, 21, 7, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 42, 42, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 382) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 42, 49, 21, 21, 21, 21, 21, 7, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 42, 42, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 383) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 40, 49, 21, 21, 21, 21, 21, 9, 1, 10, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 40, 40, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 384) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 40, 49, 21, 21, 21, 21, 21, 9, 1, 10, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 40, 40, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471977975 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 Building ZINC001471977975 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471977975 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 381) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 42, 49, 21, 21, 21, 21, 21, 7, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 42, 42, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 382) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 42, 49, 21, 21, 21, 21, 21, 7, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 42, 42, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 383) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 40, 49, 21, 21, 21, 21, 21, 9, 1, 10, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 40, 40, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 384) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 40, 49, 21, 21, 21, 21, 21, 9, 1, 10, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 40, 40, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471977975 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 Building ZINC001471977975 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471977975 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 381) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 42, 49, 21, 21, 21, 21, 21, 7, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 42, 42, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 382) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 42, 49, 21, 21, 21, 21, 21, 7, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 42, 42, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 383) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 40, 49, 21, 21, 21, 21, 21, 9, 1, 10, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 40, 40, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 384) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001471977975.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471977975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001471977975 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 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] 0 hydrogens 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, 40, 49, 21, 21, 21, 21, 21, 9, 1, 10, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 21, 21, 49, 49, 49, 49, 40, 40, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471977975 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471977975 Building ZINC001471978062 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471978062 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/385 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 26, 26, 26, 26, 26, 11, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50, 50, 46, 46, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/386 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/386' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 25, 25, 25, 25, 25, 11, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 47, 47, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/387 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/387' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 26, 26, 26, 26, 26, 11, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50, 50, 46, 46, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/388 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/388' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 25, 25, 25, 25, 25, 11, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 47, 47, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471978062 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 Building ZINC001471978062 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471978062 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 385) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 26, 26, 26, 26, 26, 11, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50, 50, 46, 46, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 386) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 25, 25, 25, 25, 25, 11, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 47, 47, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 387) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 26, 26, 26, 26, 26, 11, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50, 50, 46, 46, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 388) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 25, 25, 25, 25, 25, 11, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 47, 47, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471978062 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 Building ZINC001471978062 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471978062 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 385) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 26, 26, 26, 26, 26, 11, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50, 50, 46, 46, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 386) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 25, 25, 25, 25, 25, 11, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 47, 47, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 387) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 26, 26, 26, 26, 26, 11, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50, 50, 46, 46, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 388) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 25, 25, 25, 25, 25, 11, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 47, 47, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471978062 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 Building ZINC001471978062 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471978062 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 385) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 26, 26, 26, 26, 26, 11, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50, 50, 46, 46, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 386) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 25, 25, 25, 25, 25, 11, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 47, 47, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 387) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 26, 26, 26, 26, 26, 11, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50, 50, 46, 46, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 388) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1) `ZINC001471978062.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471978062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001471978062 none CNC(=O)CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 50, 25, 25, 25, 25, 25, 11, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 47, 47, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471978062 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471978062 Building ZINC001471983491 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471983491 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/389 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(C)(=O)=NCCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001471983491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471983491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471983491 none CS(C)(=O)=NCCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o', 'C.3', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 19, 18, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 10, 10, 7, 10, 10, 7, 28, 28, 28, 28, 28, 28, 19, 19, 18, 18, 4, 7, 10, 10, 10, 10, 10, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/390 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(C)(=O)=NCCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001471983491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471983491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471983491 none CS(C)(=O)=NCCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o', 'C.3', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 15, 14, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 11, 11, 9, 11, 11, 9, 28, 28, 28, 28, 28, 28, 15, 15, 14, 14, 4, 9, 11, 11, 9, 11, 11, 9] 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471983491 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491 Building ZINC001471983491 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471983491 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 389) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(C)(=O)=NCCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001471983491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471983491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471983491 none CS(C)(=O)=NCCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o', 'C.3', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 19, 18, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 10, 10, 7, 10, 10, 7, 28, 28, 28, 28, 28, 28, 19, 19, 18, 18, 4, 7, 10, 10, 10, 10, 10, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 390) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(C)(=O)=NCCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001471983491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471983491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471983491 none CS(C)(=O)=NCCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.o', 'C.3', 'O.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 15, 14, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 11, 11, 9, 11, 11, 9, 28, 28, 28, 28, 28, 28, 15, 15, 14, 14, 4, 9, 11, 11, 9, 11, 11, 9] 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001471983491 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001471983491 Building ZINC001472056069 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472056069 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/391 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc2nnc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)n2n1) `ZINC001472056069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472056069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472056069 none CN(C)c1ccc2nnc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)n2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'N.2', '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, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 46, 50, 46, 46, 46, 46, 46, 46, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 50, 50, 50, 50, 50, 50, 46, 46, 14, 14, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/392 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/392' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc2nnc(CNC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)n2n1) `ZINC001472056069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472056069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472056069 none CN(C)c1ccc2nnc(CNC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)n2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'N.2', '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, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 44, 50, 44, 44, 44, 44, 44, 44, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 44, 50, 50, 50, 50, 50, 50, 44, 44, 13, 13, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472056069 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069 Building ZINC001472056069 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472056069 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 391) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc2nnc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)n2n1) `ZINC001472056069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472056069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472056069 none CN(C)c1ccc2nnc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)n2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'N.2', '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, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 46, 50, 46, 46, 46, 46, 46, 46, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 50, 50, 50, 50, 50, 50, 46, 46, 14, 14, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 392) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc2nnc(CNC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)n2n1) `ZINC001472056069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472056069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472056069 none CN(C)c1ccc2nnc(CNC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)n2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'N.2', '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, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 44, 50, 44, 44, 44, 44, 44, 44, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 44, 50, 50, 50, 50, 50, 50, 44, 44, 13, 13, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472056069 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472056069 Building ZINC001472080710 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472080710 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/393 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N[C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001472080710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472080710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001472080710 none O=C(N1CC(N[C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 10, 10, 10, 29, 40, 40, 40, 40, 40, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 24, 40, 40, 40, 40, 40, 40, 10, 10, 5, 5, 5, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/394 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/394' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N[C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001472080710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472080710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001472080710 none O=C(N1CC(N[C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 8, 8, 8, 25, 35, 35, 35, 35, 35, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 8, 8, 8, 16, 35, 35, 35, 35, 35, 35, 8, 8, 4, 6, 6, 4, 6, 6, 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, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472080710 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710 Building ZINC001472080710 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472080710 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 393) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(N[C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001472080710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472080710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001472080710 none O=C(N1CC(N[C@H]2CCOC2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 10, 10, 10, 29, 40, 40, 40, 40, 40, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 24, 40, 40, 40, 40, 40, 40, 10, 10, 5, 5, 5, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 394) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(N[C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001472080710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472080710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001472080710 none O=C(N1CC(N[C@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 8, 8, 8, 25, 35, 35, 35, 35, 35, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 8, 8, 8, 16, 35, 35, 35, 35, 35, 35, 8, 8, 4, 6, 6, 4, 6, 6, 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, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472080710 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080710 Building ZINC001472080711 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472080711 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/395 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N[C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001472080711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472080711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001472080711 none O=C(N1CC(N[C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 10, 10, 10, 26, 36, 36, 36, 36, 36, 10, 1, 1, 1, 5, 5, 5, 5, 6, 6, 5, 6, 6, 5, 10, 10, 10, 20, 36, 36, 36, 36, 36, 36, 10, 10, 5, 6, 6, 5, 6, 6, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/396 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N[C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001472080711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472080711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001472080711 none O=C(N1CC(N[C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 8, 8, 8, 24, 33, 33, 33, 33, 33, 8, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 8, 8, 8, 18, 33, 33, 33, 33, 33, 33, 8, 8, 4, 5, 5, 4, 5, 5, 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, 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/83982/xcb-8058097.54/working/building/ZINC001472080711 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472080711 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711 Building ZINC001472080711 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472080711 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 395) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(N[C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001472080711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472080711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001472080711 none O=C(N1CC(N[C@@H]2CCOC2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 10, 10, 10, 26, 36, 36, 36, 36, 36, 10, 1, 1, 1, 5, 5, 5, 5, 6, 6, 5, 6, 6, 5, 10, 10, 10, 20, 36, 36, 36, 36, 36, 36, 10, 10, 5, 6, 6, 5, 6, 6, 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, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 396) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(N[C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001472080711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472080711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001472080711 none O=C(N1CC(N[C@@H]2CCOC2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 8, 8, 8, 24, 33, 33, 33, 33, 33, 8, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 8, 8, 8, 18, 33, 33, 33, 33, 33, 33, 8, 8, 4, 5, 5, 4, 5, 5, 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, 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/83982/xcb-8058097.54/working/building/ZINC001472080711 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472080711 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472080711 Building ZINC001472115896 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472115896 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/397 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cn1cncn1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001472115896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472115896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001472115896 none COC(=O)[C@@H](Cn1cncn1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 19, 4, 11, 11, 24, 35, 35, 35, 35, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 19, 19, 19, 24, 24, 35, 35, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/398 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/398' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cn1cncn1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001472115896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472115896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001472115896 none COC(=O)[C@@H](Cn1cncn1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 22, 4, 11, 11, 26, 32, 32, 32, 32, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 26, 26, 32, 32, 4, 8, 8] 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472115896 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896 Building ZINC001472115896 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472115896 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 397) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cn1cncn1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001472115896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472115896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001472115896 none COC(=O)[C@@H](Cn1cncn1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 19, 4, 11, 11, 24, 35, 35, 35, 35, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 19, 19, 19, 24, 24, 35, 35, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 398) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cn1cncn1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001472115896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472115896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001472115896 none COC(=O)[C@@H](Cn1cncn1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 22, 4, 11, 11, 26, 32, 32, 32, 32, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 26, 26, 32, 32, 4, 8, 8] 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472115896 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115896 Building ZINC001472115897 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472115897 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/399 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cn1cncn1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001472115897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472115897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001472115897 none COC(=O)[C@H](Cn1cncn1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 22, 4, 11, 11, 26, 33, 33, 33, 33, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 26, 26, 33, 33, 4, 8, 8] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/400 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cn1cncn1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001472115897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472115897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001472115897 none COC(=O)[C@H](Cn1cncn1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 20, 4, 12, 12, 24, 35, 35, 35, 35, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 20, 20, 20, 24, 24, 35, 35, 4, 9, 9] 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472115897 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897 Building ZINC001472115897 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472115897 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 399) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cn1cncn1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001472115897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472115897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001472115897 none COC(=O)[C@H](Cn1cncn1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 22, 4, 11, 11, 26, 33, 33, 33, 33, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 26, 26, 33, 33, 4, 8, 8] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 400) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cn1cncn1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001472115897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472115897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001472115897 none COC(=O)[C@H](Cn1cncn1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 20, 4, 12, 12, 24, 35, 35, 35, 35, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 20, 20, 20, 24, 24, 35, 35, 4, 9, 9] 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472115897 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472115897 Building ZINC001472259328 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472259328 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/401 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1O) `ZINC001472259328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472259328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472259328 none COc1cnc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'O.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, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 4, 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: [29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 58] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/402 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1O) `ZINC001472259328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472259328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472259328 none COc1cnc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'O.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, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [43, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 32, 32, 32, 43, 43, 43, 32, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 64] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472259328 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328 Building ZINC001472259328 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472259328 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 401) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1O) `ZINC001472259328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472259328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472259328 none COc1cnc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'O.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, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 4, 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: [29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 58] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 402) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1O) `ZINC001472259328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472259328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472259328 none COc1cnc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'O.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, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [43, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 32, 32, 32, 43, 43, 43, 32, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 64] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472259328 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259328 Building ZINC001472259329 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472259329 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/403 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1O) `ZINC001472259329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472259329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472259329 none COc1cnc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'O.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, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 4, 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: [42, 33, 33, 33, 33, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 33, 33, 33, 42, 42, 42, 33, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 66] 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]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/404 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/404' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1O) `ZINC001472259329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472259329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472259329 none COc1cnc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'O.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, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 4, 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: [29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 58] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472259329 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329 Building ZINC001472259329 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472259329 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 403) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1O) `ZINC001472259329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472259329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472259329 none COc1cnc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'O.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, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 4, 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: [42, 33, 33, 33, 33, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 33, 33, 33, 42, 42, 42, 33, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 66] 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]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 404) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1O) `ZINC001472259329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472259329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472259329 none COc1cnc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'O.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, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 4, 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: [29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 58] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472259329 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472259329 Building ZINC001472278876 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472278876 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/405 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCCn2ccc(O)nc2=O)cn1) `ZINC001472278876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472278876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001472278876 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCCn2ccc(O)nc2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 12, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 2, 2, 2, 16, 14, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 16, 16, 22, 22, 24, 23, 26, 26, 78, 6] 150 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: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/406 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/406' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCCn2ccc(O)nc2=O)cn1) `ZINC001472278876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472278876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001472278876 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCCn2ccc(O)nc2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 12, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 16, 16, 24, 24, 26, 25, 28, 28, 84, 6] 150 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: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472278876 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876 Building ZINC001472278876 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472278876 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 405) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCCn2ccc(O)nc2=O)cn1) `ZINC001472278876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472278876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001472278876 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCCn2ccc(O)nc2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 12, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 2, 2, 2, 16, 14, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 16, 16, 22, 22, 24, 23, 26, 26, 78, 6] 150 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: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 406) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCCn2ccc(O)nc2=O)cn1) `ZINC001472278876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472278876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001472278876 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCCn2ccc(O)nc2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 12, 8, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 16, 16, 24, 24, 26, 25, 28, 28, 84, 6] 150 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: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472278876 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278876 Building ZINC001472278936 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472278936 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/407 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCn1ccc(O)nc1=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001472278936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472278936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001472278936 none O=C(NCCCn1ccc(O)nc1=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 18, 24, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 18, 18, 34, 34, 41, 41, 50, 50, 150, 3, 3, 3, 3] 150 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]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/408 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCn1ccc(O)nc1=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001472278936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472278936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001472278936 none O=C(NCCCn1ccc(O)nc1=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 18, 25, 45, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 33, 33, 40, 41, 50, 50, 150, 3, 3, 3, 3] 150 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]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472278936 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936 Building ZINC001472278936 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472278936 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 407) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCn1ccc(O)nc1=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001472278936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472278936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001472278936 none O=C(NCCCn1ccc(O)nc1=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 18, 24, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 18, 18, 34, 34, 41, 41, 50, 50, 150, 3, 3, 3, 3] 150 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]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 408) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCn1ccc(O)nc1=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001472278936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472278936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001472278936 none O=C(NCCCn1ccc(O)nc1=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 18, 25, 45, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 33, 33, 40, 41, 50, 50, 150, 3, 3, 3, 3] 150 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]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472278936 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472278936 Building ZINC001472294633 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472294633 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/409 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(C2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)[nH]n1) `ZINC001472294633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472294633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001472294633 none COC(=O)c1cc(C2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 34, 22, 22, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 22, 22, 22, 34, 34, 34, 22, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/410 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/410' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(C2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)[nH]n1) `ZINC001472294633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472294633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001472294633 none COC(=O)c1cc(C2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 20, 32, 20, 20, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 20, 20, 20, 32, 32, 32, 20, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472294633 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633 Building ZINC001472294633 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472294633 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 409) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(C2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)[nH]n1) `ZINC001472294633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472294633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001472294633 none COC(=O)c1cc(C2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 34, 22, 22, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 22, 22, 22, 34, 34, 34, 22, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 410) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(C2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)[nH]n1) `ZINC001472294633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472294633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001472294633 none COC(=O)c1cc(C2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 20, 32, 20, 20, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 20, 20, 20, 32, 32, 32, 20, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472294633 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472294633 Building ZINC001472302186 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472302186 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/411 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1cn(C2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)nn1) `ZINC001472302186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472302186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001472302186 none CC(=O)c1cn(C2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 8, 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, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 30, 42, 30, 30, 5, 5, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 30, 30, 42, 42, 42, 30, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/412 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/412' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1cn(C2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)nn1) `ZINC001472302186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472302186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001472302186 none CC(=O)c1cn(C2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 8, 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, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 31, 24, 24, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 24, 24, 31, 31, 31, 24, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472302186 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186 Building ZINC001472302186 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472302186 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 411) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1cn(C2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)nn1) `ZINC001472302186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472302186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001472302186 none CC(=O)c1cn(C2CN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 8, 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, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 30, 42, 30, 30, 5, 5, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 30, 30, 42, 42, 42, 30, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 412) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1cn(C2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)nn1) `ZINC001472302186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472302186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001472302186 none CC(=O)c1cn(C2CN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 8, 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, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 31, 24, 24, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 24, 24, 31, 31, 31, 24, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472302186 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472302186 Building ZINC001472494164 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472494164 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/413 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001472494164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472494164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001472494164 none NS(=O)(=O)CCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 14, 14, 10, 7, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 11, 11, 11, 11, 7, 7, 5, 7, 7, 7, 7] 22 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/414 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/414' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001472494164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472494164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001472494164 none NS(=O)(=O)CCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 14, 14, 10, 7, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 11, 11, 11, 11, 7, 7, 5, 7, 7, 7, 7] 22 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472494164 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164 Building ZINC001472494164 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472494164 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 413) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001472494164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472494164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001472494164 none NS(=O)(=O)CCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 14, 14, 10, 7, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 11, 11, 11, 11, 7, 7, 5, 7, 7, 7, 7] 22 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 414) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001472494164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472494164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001472494164 none NS(=O)(=O)CCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 14, 14, 10, 7, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 11, 11, 11, 11, 7, 7, 5, 7, 7, 7, 7] 22 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472494164 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472494164 Building ZINC001472583210 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472583210 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/415 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ncnc2c1ncn2CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001472583210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472583210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001472583210 none Nc1ncnc2c1ncn2CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 8, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 27, 27, 16, 16, 3, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/416 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ncnc2c1ncn2CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001472583210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472583210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001472583210 none Nc1ncnc2c1ncn2CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 8, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 26, 26, 15, 15, 2, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472583210 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210 Building ZINC001472583210 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472583210 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 415) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ncnc2c1ncn2CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001472583210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472583210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001472583210 none Nc1ncnc2c1ncn2CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 8, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 27, 27, 16, 16, 3, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 416) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ncnc2c1ncn2CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001472583210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472583210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001472583210 none Nc1ncnc2c1ncn2CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 8, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 26, 26, 15, 15, 2, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472583210 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472583210 Building ZINC001472943100 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472943100 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/417 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001472943100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472943100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001472943100 none C[C@H](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 1, 8, 1, 1, 1, 8, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 12, 35, 35, 49, 49, 50, 50, 50, 50, 50, 50, 12, 12, 12, 6, 1, 3, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 35, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/418 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001472943100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472943100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001472943100 none C[C@H](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 1, 8, 1, 1, 1, 8, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 34, 34, 49, 49, 50, 50, 50, 50, 50, 50, 11, 11, 11, 6, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 34, 34, 34, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472943100 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100 Building ZINC001472943100 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472943100 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 417) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001472943100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472943100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001472943100 none C[C@H](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 1, 8, 1, 1, 1, 8, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 12, 35, 35, 49, 49, 50, 50, 50, 50, 50, 50, 12, 12, 12, 6, 1, 3, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 35, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 418) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001472943100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472943100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001472943100 none C[C@H](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 1, 8, 1, 1, 1, 8, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 34, 34, 49, 49, 50, 50, 50, 50, 50, 50, 11, 11, 11, 6, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 34, 34, 34, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472943100 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943100 Building ZINC001472943101 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472943101 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/419 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001472943101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472943101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001472943101 none C[C@@H](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 1, 8, 1, 1, 1, 8, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 30, 30, 49, 49, 50, 50, 50, 50, 50, 50, 11, 11, 11, 6, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 30, 30, 30, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/420 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001472943101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472943101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001472943101 none C[C@@H](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 1, 8, 1, 1, 1, 8, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 32, 32, 49, 49, 50, 50, 50, 50, 50, 50, 10, 10, 10, 6, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 32, 32, 32, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472943101 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101 Building ZINC001472943101 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472943101 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 419) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001472943101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472943101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001472943101 none C[C@@H](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 1, 8, 1, 1, 1, 8, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 30, 30, 49, 49, 50, 50, 50, 50, 50, 50, 11, 11, 11, 6, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 30, 30, 30, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 420) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001472943101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472943101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001472943101 none C[C@@H](C(=O)Nc1ncccn1)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 1, 8, 1, 1, 1, 8, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 32, 32, 49, 49, 50, 50, 50, 50, 50, 50, 10, 10, 10, 6, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 32, 32, 32, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472943101 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943101 Building ZINC001472943137 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472943137 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/421 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2nnc3n2CCCC3)CC1) `ZINC001472943137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472943137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001472943137 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2nnc3n2CCCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 12, 13, 13, 13, 13, 25, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/422 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(Cc2nnc3n2CCCC3)CC1) `ZINC001472943137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472943137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001472943137 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(Cc2nnc3n2CCCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 12, 13, 13, 13, 13, 24, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472943137 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137 Building ZINC001472943137 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472943137 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 421) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2nnc3n2CCCC3)CC1) `ZINC001472943137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472943137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001472943137 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2nnc3n2CCCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 12, 13, 13, 13, 13, 25, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 422) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(Cc2nnc3n2CCCC3)CC1) `ZINC001472943137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472943137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001472943137 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(Cc2nnc3n2CCCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 12, 13, 13, 13, 13, 24, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472943137 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943137 Building ZINC001472943747 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472943747 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/423 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCn1nnnc1CN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001472943747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472943747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001472943747 none CCCCn1nnnc1CN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 21, 21, 21, 21, 21, 13, 6, 6, 6, 6, 5, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 50, 50, 40, 40, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/424 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/424' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCn1nnnc1CN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001472943747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472943747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001472943747 none CCCCn1nnnc1CN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 22, 22, 22, 22, 22, 13, 5, 5, 5, 5, 4, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50, 50, 40, 40, 13, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472943747 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747 Building ZINC001472943747 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472943747 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 423) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCn1nnnc1CN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001472943747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472943747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001472943747 none CCCCn1nnnc1CN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 21, 21, 21, 21, 21, 13, 6, 6, 6, 6, 5, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 50, 50, 40, 40, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 424) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCn1nnnc1CN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001472943747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472943747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001472943747 none CCCCn1nnnc1CN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 22, 22, 22, 22, 22, 13, 5, 5, 5, 5, 4, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50, 50, 40, 40, 13, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472943747 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943747 Building ZINC001472943870 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472943870 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/425 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)on1) `ZINC001472943870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472943870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472943870 none Cc1cc(NC(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 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, 34, 34, 22, 34, 8, 8, 8, 8, 6, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 34, 22, 22, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/426 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/426' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)on1) `ZINC001472943870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472943870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472943870 none Cc1cc(NC(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 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, 33, 33, 23, 33, 8, 8, 8, 8, 6, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 33, 23, 23, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/83982/xcb-8058097.54/working/building/ZINC001472943870 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472943870 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870 Building ZINC001472943870 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472943870 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 425) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)on1) `ZINC001472943870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472943870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472943870 none Cc1cc(NC(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 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, 34, 34, 22, 34, 8, 8, 8, 8, 6, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 34, 22, 22, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 426) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)on1) `ZINC001472943870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472943870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001472943870 none Cc1cc(NC(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 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, 33, 33, 23, 33, 8, 8, 8, 8, 6, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 33, 23, 23, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/83982/xcb-8058097.54/working/building/ZINC001472943870 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472943870 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472943870 Building ZINC001472944003 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472944003 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/427 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CC[C@@H]2CCS(=O)(=O)C2)CC1) `ZINC001472944003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472944003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001472944003 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CC[C@@H]2CCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 16, 37, 50, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 25, 25, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/428 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/428' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CC[C@@H]2CCS(=O)(=O)C2)CC1) `ZINC001472944003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472944003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001472944003 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CC[C@@H]2CCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 16, 38, 50, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 25, 25, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472944003 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003 Building ZINC001472944003 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472944003 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 427) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CC[C@@H]2CCS(=O)(=O)C2)CC1) `ZINC001472944003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472944003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001472944003 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CC[C@@H]2CCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 16, 37, 50, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 25, 25, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 428) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CC[C@@H]2CCS(=O)(=O)C2)CC1) `ZINC001472944003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472944003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001472944003 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CC[C@@H]2CCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 16, 38, 50, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 25, 25, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472944003 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944003 Building ZINC001472944004 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472944004 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/429 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CC[C@H]2CCS(=O)(=O)C2)CC1) `ZINC001472944004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472944004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001472944004 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CC[C@H]2CCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 18, 38, 50, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 18, 18, 28, 28, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/430 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CC[C@H]2CCS(=O)(=O)C2)CC1) `ZINC001472944004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472944004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001472944004 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CC[C@H]2CCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 19, 37, 50, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 28, 28, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472944004 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004 Building ZINC001472944004 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472944004 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 429) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CC[C@H]2CCS(=O)(=O)C2)CC1) `ZINC001472944004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472944004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001472944004 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CC[C@H]2CCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 18, 38, 50, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 18, 18, 28, 28, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 430) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CC[C@H]2CCS(=O)(=O)C2)CC1) `ZINC001472944004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472944004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001472944004 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CC[C@H]2CCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 19, 37, 50, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 28, 28, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001472944004 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001472944004 Building ZINC001496050681 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001496050681 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/431 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)C(=O)NCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001496050681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001496050681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001496050681 none CC1CCN(C(=O)C(=O)NCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 21, 41, 20, 20, 10, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 10, 10, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/432 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/432' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)C(=O)NCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001496050681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001496050681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001496050681 none CC1CCN(C(=O)C(=O)NCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 22, 39, 21, 21, 10, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 10, 10, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001496050681 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681 Building ZINC001496050681 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001496050681 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 431) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)C(=O)NCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001496050681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001496050681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001496050681 none CC1CCN(C(=O)C(=O)NCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 21, 41, 20, 20, 10, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 10, 10, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 432) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)C(=O)NCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001496050681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001496050681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001496050681 none CC1CCN(C(=O)C(=O)NCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 22, 39, 21, 21, 10, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 10, 10, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001496050681 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001496050681 Building ZINC001479286679 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479286679 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/433 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)NCCN[C@H]1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001479286679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479286679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479286679 none CC(C)NC(=O)NCCN[C@H]1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 41, 35, 29, 29, 29, 29, 15, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 41, 41, 35, 29, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/434 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/434' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)NCCN[C@H]1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001479286679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479286679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479286679 none CC(C)NC(=O)NCCN[C@H]1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 42, 33, 27, 27, 27, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 42, 42, 33, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479286679 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679 Building ZINC001479286679 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479286679 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 433) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)NCCN[C@H]1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001479286679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479286679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479286679 none CC(C)NC(=O)NCCN[C@H]1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 41, 35, 29, 29, 29, 29, 15, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 41, 41, 35, 29, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 434) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)NCCN[C@H]1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001479286679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479286679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479286679 none CC(C)NC(=O)NCCN[C@H]1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 42, 33, 27, 27, 27, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 42, 42, 33, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479286679 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479286679 Building ZINC001479358143 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479358143 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/435 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CN[C@H]2C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1=O) `ZINC001479358143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479358143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479358143 none Cn1ccc(CN[C@H]2C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 10, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 40, 27, 27, 27, 27, 12, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 40, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/436 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CN[C@H]2C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1=O) `ZINC001479358143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479358143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479358143 none Cn1ccc(CN[C@H]2C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 10, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 40, 28, 28, 28, 28, 12, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 40, 28, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479358143 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143 Building ZINC001479358143 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479358143 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 435) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CN[C@H]2C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1=O) `ZINC001479358143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479358143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479358143 none Cn1ccc(CN[C@H]2C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 10, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 40, 27, 27, 27, 27, 12, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 40, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 436) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CN[C@H]2C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1=O) `ZINC001479358143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479358143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479358143 none Cn1ccc(CN[C@H]2C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 10, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 40, 28, 28, 28, 28, 12, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 40, 28, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479358143 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479358143 Building ZINC001479438983 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479438983 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/437 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O) `ZINC001479438983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479438983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479438983 none C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 34, 34, 34, 34, 34, 14, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 42, 50, 50, 50, 42, 50, 42, 42, 42, 42, 34, 34, 34, 34, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 42] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/438 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/438' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O) `ZINC001479438983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479438983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479438983 none C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 35, 35, 35, 35, 35, 16, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 42, 50, 50, 50, 42, 50, 42, 42, 42, 42, 35, 35, 35, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 42] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479438983 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983 Building ZINC001479438983 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479438983 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 437) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O) `ZINC001479438983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479438983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479438983 none C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 34, 34, 34, 34, 34, 14, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 42, 50, 50, 50, 42, 50, 42, 42, 42, 42, 34, 34, 34, 34, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 42] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 438) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O) `ZINC001479438983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479438983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479438983 none C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 35, 35, 35, 35, 35, 16, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 42, 50, 50, 50, 42, 50, 42, 42, 42, 42, 35, 35, 35, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 42] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479438983 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438983 Building ZINC001479438985 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479438985 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/439 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O) `ZINC001479438985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479438985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479438985 none C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 34, 34, 34, 34, 34, 11, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 44, 50, 50, 50, 46, 50, 44, 44, 44, 44, 34, 34, 34, 34, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 48] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 46, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/440 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O) `ZINC001479438985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479438985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479438985 none C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 44, 44, 44, 44, 44, 22, 44, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 44, 48, 50, 50, 50, 48, 50, 48, 48, 48, 48, 44, 44, 44, 44, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479438985 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985 Building ZINC001479438985 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479438985 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 439) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O) `ZINC001479438985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479438985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479438985 none C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 34, 34, 34, 34, 34, 11, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 44, 50, 50, 50, 46, 50, 44, 44, 44, 44, 34, 34, 34, 34, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 48] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 46, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 440) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O) `ZINC001479438985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479438985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479438985 none C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 44, 44, 44, 44, 44, 22, 44, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 44, 48, 50, 50, 50, 48, 50, 48, 48, 48, 48, 44, 44, 44, 44, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479438985 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479438985 Building ZINC001479556349 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479556349 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/441 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNCCOCCO)C1) `ZINC001479556349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479556349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479556349 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNCCOCCO)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 19, 20, 39, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 13, 19, 19, 20, 20, 50, 50, 50, 50, 150, 2, 2] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 328 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/442 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/442' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNCCOCCO)C1) `ZINC001479556349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479556349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479556349 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNCCOCCO)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 21, 29, 29, 42, 50, 50, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 21, 29, 29, 29, 29, 50, 50, 50, 50, 150, 5, 5] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479556349 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349 Building ZINC001479556349 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479556349 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 441) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)[C@H](CNCCOCCO)C1) `ZINC001479556349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479556349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479556349 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNCCOCCO)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 19, 20, 39, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 13, 19, 19, 20, 20, 50, 50, 50, 50, 150, 2, 2] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 328 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 442) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)[C@H](CNCCOCCO)C1) `ZINC001479556349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479556349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479556349 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNCCOCCO)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 21, 29, 29, 42, 50, 50, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 21, 29, 29, 29, 29, 50, 50, 50, 50, 150, 5, 5] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479556349 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479556349 Building ZINC001479632750 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479632750 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/443 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 46, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/444 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/444' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 46, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/445 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/445' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 45, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/446 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/446' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 45, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479632750 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 Building ZINC001479632750 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479632750 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 443) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 46, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 444) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 46, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 445) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 45, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 446) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 45, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479632750 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 Building ZINC001479632750 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479632750 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 443) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 46, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 444) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 46, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 445) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 45, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 446) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 45, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479632750 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 Building ZINC001479632750 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479632750 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 443) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 46, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 444) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 46, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 445) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 45, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 446) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1) `ZINC001479632750.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479632750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479632750 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1nc(=O)n(C)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 11, 8, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 25, 25, 25, 6, 25, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 45, 45, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479632750 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479632750 Building ZINC001479666113 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479666113 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/447 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 26, 39, 39, 16, 16, 16, 16, 16, 16, 15, 6, 1, 10, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 117, 26, 26, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 345 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/448 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/448' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 19, 31, 31, 11, 11, 11, 11, 11, 11, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 93, 19, 19, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 323 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/449 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/449' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 26, 39, 39, 16, 16, 16, 16, 16, 16, 15, 6, 1, 10, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 117, 26, 26, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 345 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/450 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/450' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 19, 31, 31, 11, 11, 11, 11, 11, 11, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 93, 19, 19, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 323 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479666113 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 Building ZINC001479666113 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479666113 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 447) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 26, 39, 39, 16, 16, 16, 16, 16, 16, 15, 6, 1, 10, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 117, 26, 26, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 345 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 448) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 19, 31, 31, 11, 11, 11, 11, 11, 11, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 93, 19, 19, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 323 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 449) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 26, 39, 39, 16, 16, 16, 16, 16, 16, 15, 6, 1, 10, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 117, 26, 26, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 345 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 450) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 19, 31, 31, 11, 11, 11, 11, 11, 11, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 93, 19, 19, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 323 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479666113 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 Building ZINC001479666113 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479666113 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 447) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 26, 39, 39, 16, 16, 16, 16, 16, 16, 15, 6, 1, 10, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 117, 26, 26, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 345 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 448) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 19, 31, 31, 11, 11, 11, 11, 11, 11, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 93, 19, 19, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 323 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 449) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 26, 39, 39, 16, 16, 16, 16, 16, 16, 15, 6, 1, 10, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 117, 26, 26, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 345 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 450) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 19, 31, 31, 11, 11, 11, 11, 11, 11, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 93, 19, 19, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 323 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479666113 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 Building ZINC001479666113 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479666113 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 447) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 26, 39, 39, 16, 16, 16, 16, 16, 16, 15, 6, 1, 10, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 117, 26, 26, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 345 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 448) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 19, 31, 31, 11, 11, 11, 11, 11, 11, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 93, 19, 19, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 323 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 449) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 39, 26, 39, 39, 16, 16, 16, 16, 16, 16, 15, 6, 1, 10, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 117, 26, 26, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 345 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 450) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001479666113.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479666113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479666113 none COC[C@H](O)CN1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 31, 19, 31, 31, 11, 11, 11, 11, 11, 11, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 93, 19, 19, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 323 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479666113 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479666113 Building ZINC001479676389 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676389 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/451 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 26, 20, 26, 20, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 26, 26, 26, 20, 20, 20, 20, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/452 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/452' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 26, 20, 26, 20, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 26, 26, 26, 20, 20, 20, 20, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/453 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/453' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 24, 18, 24, 18, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 34, 24, 24, 24, 18, 18, 18, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/454 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/454' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 24, 18, 24, 18, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 34, 24, 24, 24, 18, 18, 18, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676389 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 Building ZINC001479676389 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676389 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 451) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 26, 20, 26, 20, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 26, 26, 26, 20, 20, 20, 20, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 452) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 26, 20, 26, 20, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 26, 26, 26, 20, 20, 20, 20, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 453) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 24, 18, 24, 18, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 34, 24, 24, 24, 18, 18, 18, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 454) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 24, 18, 24, 18, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 34, 24, 24, 24, 18, 18, 18, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676389 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 Building ZINC001479676389 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676389 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 451) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 26, 20, 26, 20, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 26, 26, 26, 20, 20, 20, 20, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 452) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 26, 20, 26, 20, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 26, 26, 26, 20, 20, 20, 20, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 453) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 24, 18, 24, 18, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 34, 24, 24, 24, 18, 18, 18, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 454) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 24, 18, 24, 18, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 34, 24, 24, 24, 18, 18, 18, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676389 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 Building ZINC001479676389 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676389 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 451) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 26, 20, 26, 20, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 26, 26, 26, 20, 20, 20, 20, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 452) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 26, 20, 26, 20, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 35, 35, 26, 26, 26, 20, 20, 20, 20, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 453) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 24, 18, 24, 18, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 34, 24, 24, 24, 18, 18, 18, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 454) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001479676389.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676389 none Cc1nc(CN(C)CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 24, 18, 24, 18, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 34, 34, 24, 24, 24, 18, 18, 18, 18, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676389 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676389 Building ZINC001479676879 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676879 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/455 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 26, 26, 14, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 26, 26, 26, 26, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/456 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/456' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 26, 26, 11, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 26, 26, 26, 26, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/457 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/457' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 26, 26, 14, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 26, 26, 26, 26, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/458 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/458' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 26, 26, 11, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 26, 26, 26, 26, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676879 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 Building ZINC001479676879 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676879 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 455) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 26, 26, 14, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 26, 26, 26, 26, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 456) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 26, 26, 11, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 26, 26, 26, 26, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 457) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 26, 26, 14, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 26, 26, 26, 26, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 458) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 26, 26, 11, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 26, 26, 26, 26, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676879 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 Building ZINC001479676879 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676879 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 455) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 26, 26, 14, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 26, 26, 26, 26, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 456) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 26, 26, 11, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 26, 26, 26, 26, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 457) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 26, 26, 14, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 26, 26, 26, 26, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 458) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 26, 26, 11, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 26, 26, 26, 26, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676879 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 Building ZINC001479676879 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676879 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 455) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 26, 26, 14, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 26, 26, 26, 26, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 456) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 26, 26, 11, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 26, 26, 26, 26, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 457) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 26, 26, 14, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 26, 26, 26, 26, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 458) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1) `ZINC001479676879.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479676879 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 26, 26, 11, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 26, 26, 26, 26, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676879 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676879 Building ZINC001479676890 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676890 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/459 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 49, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/460 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 19, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/461 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/461' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 49, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/462 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/462' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 19, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676890 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 Building ZINC001479676890 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676890 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 459) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 49, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 460) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 19, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 461) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 49, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 462) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 19, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676890 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 Building ZINC001479676890 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676890 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 459) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 49, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 460) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 19, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 461) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 49, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 462) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 19, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676890 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 Building ZINC001479676890 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676890 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 459) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 49, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 460) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 19, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 461) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 20, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 49, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 462) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1) `ZINC001479676890.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676890 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1cn(C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 19, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 40, 40, 40, 31, 31, 31, 31, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676890 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676890 Building ZINC001479676921 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676921 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/463 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/464 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/465 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/465' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/466 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/466' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676921 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 Building ZINC001479676921 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676921 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 463) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 464) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 465) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 466) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676921 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 Building ZINC001479676921 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676921 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 463) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 464) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 465) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 466) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676921 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 Building ZINC001479676921 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479676921 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 463) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 464) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 465) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 466) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C) `ZINC001479676921.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479676921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001479676921 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ncnn1C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 1, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 37, 21, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 38, 38, 37, 37, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479676921 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479676921 Building ZINC001479683226 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479683226 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/467 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCC(=O)NC(N)=O)C1) `ZINC001479683226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479683226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479683226 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCC(=O)NC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 10, 5, 1, 11, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 8, 9, 9, 9, 9, 9, 9, 9, 9, 14, 33, 50, 50, 50, 34, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 33, 33, 50, 50, 34, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/468 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/468' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCC(=O)NC(N)=O)C1) `ZINC001479683226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479683226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479683226 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCC(=O)NC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 10, 5, 1, 11, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 6, 6, 6, 6, 6, 6, 6, 14, 28, 50, 50, 50, 28, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 28, 28, 50, 50, 28, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479683226 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226 Building ZINC001479683226 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479683226 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 467) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CCCCC[C@@H](NCC(=O)NC(N)=O)C1) `ZINC001479683226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479683226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479683226 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCC(=O)NC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 10, 5, 1, 11, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 8, 9, 9, 9, 9, 9, 9, 9, 9, 14, 33, 50, 50, 50, 34, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 33, 33, 50, 50, 34, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 468) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CCCCC[C@@H](NCC(=O)NC(N)=O)C1) `ZINC001479683226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479683226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479683226 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCC(=O)NC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 10, 5, 1, 11, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 6, 6, 6, 6, 6, 6, 6, 14, 28, 50, 50, 50, 28, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 28, 28, 50, 50, 28, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479683226 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683226 Building ZINC001479683227 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479683227 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/469 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H](NCC(=O)NC(N)=O)C1) `ZINC001479683227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479683227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479683227 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H](NCC(=O)NC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 10, 5, 1, 11, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 32, 50, 50, 50, 32, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 32, 32, 50, 50, 34, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/470 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/470' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H](NCC(=O)NC(N)=O)C1) `ZINC001479683227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479683227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479683227 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H](NCC(=O)NC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 10, 5, 1, 11, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 30, 50, 50, 50, 30, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 30, 30, 50, 50, 30, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479683227 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227 Building ZINC001479683227 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479683227 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 469) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CCCCC[C@H](NCC(=O)NC(N)=O)C1) `ZINC001479683227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479683227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479683227 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H](NCC(=O)NC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 10, 5, 1, 11, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 32, 50, 50, 50, 32, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 32, 32, 50, 50, 34, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 470) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CCCCC[C@H](NCC(=O)NC(N)=O)C1) `ZINC001479683227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479683227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479683227 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H](NCC(=O)NC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 10, 5, 1, 11, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 30, 50, 50, 50, 30, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 30, 30, 50, 50, 30, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479683227 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479683227 Building ZINC001479701346 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479701346 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/471 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 31, 31, 31, 31, 31, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/472 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/472' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 31, 31, 31, 31, 31, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/473 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/473' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 31, 31, 31, 31, 31, 50, 50, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/474 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/474' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 31, 31, 31, 31, 31, 50, 50, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479701346 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 Building ZINC001479701346 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479701346 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 471) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 31, 31, 31, 31, 31, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 472) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 31, 31, 31, 31, 31, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 473) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 31, 31, 31, 31, 31, 50, 50, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 474) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 31, 31, 31, 31, 31, 50, 50, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479701346 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 Building ZINC001479701346 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479701346 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 471) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 31, 31, 31, 31, 31, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 472) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 31, 31, 31, 31, 31, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 473) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 31, 31, 31, 31, 31, 50, 50, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 474) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 31, 31, 31, 31, 31, 50, 50, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479701346 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 Building ZINC001479701346 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479701346 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 471) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 31, 31, 31, 31, 31, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 472) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 31, 31, 31, 31, 31, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 473) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 31, 31, 31, 31, 31, 50, 50, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 474) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF) `ZINC001479701346.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479701346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001479701346 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1Cc1ncnn1CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 8, 1, 8, 8, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 31, 31, 31, 31, 31, 50, 50, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 31, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479701346 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479701346 Building ZINC001479702269 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479702269 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/475 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 40, 21, 21, 12, 21, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 40, 40, 21, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/476 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/476' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 40, 21, 21, 12, 21, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 40, 40, 21, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/477 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/477' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 38, 23, 23, 12, 23, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 23, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/478 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/478' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 38, 23, 23, 12, 23, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 23, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479702269 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 Building ZINC001479702269 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479702269 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 475) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 40, 21, 21, 12, 21, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 40, 40, 21, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 476) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 40, 21, 21, 12, 21, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 40, 40, 21, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 477) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 38, 23, 23, 12, 23, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 23, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 478) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 38, 23, 23, 12, 23, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 23, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479702269 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 Building ZINC001479702269 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479702269 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 475) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 40, 21, 21, 12, 21, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 40, 40, 21, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 476) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 40, 21, 21, 12, 21, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 40, 40, 21, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 477) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 38, 23, 23, 12, 23, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 23, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 478) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 38, 23, 23, 12, 23, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 23, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479702269 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 Building ZINC001479702269 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479702269 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 475) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 40, 21, 21, 12, 21, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 40, 40, 21, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 476) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 40, 21, 21, 12, 21, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 40, 40, 21, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 477) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 38, 23, 23, 12, 23, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 23, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 478) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001479702269.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479702269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001479702269 none CCOCCNC(=O)CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 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] 0 hydrogens need rotated 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, 38, 23, 23, 12, 23, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 23, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479702269 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702269 Building ZINC001479702404 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479702404 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/479 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 31, 31, 31, 42, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 23, 93, 42, 42, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 296 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/480 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/480' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 31, 31, 31, 42, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 23, 93, 42, 42, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 296 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/481 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/481' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 31, 31, 31, 43, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 22, 93, 43, 43, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 301 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/482 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/482' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 31, 31, 31, 43, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 22, 93, 43, 43, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 301 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479702404 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 Building ZINC001479702404 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479702404 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 479) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 31, 31, 31, 42, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 23, 93, 42, 42, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 296 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 480) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 31, 31, 31, 42, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 23, 93, 42, 42, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 296 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 481) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 31, 31, 31, 43, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 22, 93, 43, 43, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 301 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 482) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 31, 31, 31, 43, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 22, 93, 43, 43, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 301 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479702404 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 Building ZINC001479702404 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479702404 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 479) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 31, 31, 31, 42, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 23, 93, 42, 42, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 296 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 480) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 31, 31, 31, 42, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 23, 93, 42, 42, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 296 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 481) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 31, 31, 31, 43, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 22, 93, 43, 43, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 301 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 482) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 31, 31, 31, 43, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 22, 93, 43, 43, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 301 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479702404 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 Building ZINC001479702404 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479702404 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 479) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 31, 31, 31, 42, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 23, 93, 42, 42, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 296 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 480) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 31, 31, 31, 42, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 23, 23, 93, 42, 42, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 296 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 481) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 31, 31, 31, 43, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 22, 93, 43, 43, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 301 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 482) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1) `ZINC001479702404.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479702404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702404 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 31, 31, 31, 43, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 22, 22, 93, 43, 43, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 301 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479702404 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702404 Building ZINC001479702406 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479702406 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/483 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 36, 36, 36, 45, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 21, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 323 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/484 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/484' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 36, 36, 36, 45, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 21, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 323 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/485 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/485' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 6, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 36, 36, 36, 45, 50, 50, 50, 50, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 22, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 320 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/486 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/486' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 6, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 36, 36, 36, 45, 50, 50, 50, 50, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 22, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 320 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479702406 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 Building ZINC001479702406 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479702406 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 483) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 36, 36, 36, 45, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 21, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 323 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 484) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 36, 36, 36, 45, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 21, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 323 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 485) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 6, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 36, 36, 36, 45, 50, 50, 50, 50, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 22, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 320 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 486) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 6, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 36, 36, 36, 45, 50, 50, 50, 50, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 22, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 320 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479702406 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 Building ZINC001479702406 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479702406 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 483) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 36, 36, 36, 45, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 21, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 323 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 484) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 36, 36, 36, 45, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 21, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 323 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 485) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 6, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 36, 36, 36, 45, 50, 50, 50, 50, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 22, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 320 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 486) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 6, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 36, 36, 36, 45, 50, 50, 50, 50, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 22, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 320 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479702406 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 Building ZINC001479702406 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479702406 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 483) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 36, 36, 36, 45, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 21, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 323 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 484) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 6, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 36, 36, 36, 45, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 21, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 323 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 485) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 6, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 36, 36, 36, 45, 50, 50, 50, 50, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 22, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 320 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 486) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1) `ZINC001479702406.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479702406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479702406 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 6, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 36, 36, 36, 45, 50, 50, 50, 50, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 22, 22, 108, 45, 45, 50, 50, 50] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 320 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479702406 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479702406 Building ZINC001479733664 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479733664 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/487 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 49, 49, 34, 50, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 32, 32, 49, 50, 34, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/488 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/488' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 50, 50, 50, 28, 50, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 27, 27, 50, 50, 28, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/489 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/489' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 49, 49, 34, 50, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 32, 32, 49, 50, 34, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/490 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/490' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 50, 50, 50, 28, 50, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 27, 27, 50, 50, 28, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479733664 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 Building ZINC001479733664 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479733664 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 487) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 49, 49, 34, 50, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 32, 32, 49, 50, 34, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 488) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 50, 50, 50, 28, 50, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 27, 27, 50, 50, 28, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 489) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 49, 49, 34, 50, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 32, 32, 49, 50, 34, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 490) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 50, 50, 50, 28, 50, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 27, 27, 50, 50, 28, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479733664 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 Building ZINC001479733664 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479733664 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 487) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 49, 49, 34, 50, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 32, 32, 49, 50, 34, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 488) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 50, 50, 50, 28, 50, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 27, 27, 50, 50, 28, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 489) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 49, 49, 34, 50, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 32, 32, 49, 50, 34, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 490) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 50, 50, 50, 28, 50, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 27, 27, 50, 50, 28, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479733664 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 Building ZINC001479733664 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479733664 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 487) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 49, 49, 34, 50, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 32, 32, 49, 50, 34, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 488) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 50, 50, 50, 28, 50, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 27, 27, 50, 50, 28, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 489) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 49, 49, 34, 50, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 32, 32, 49, 50, 34, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 490) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001479733664.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479733664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001479733664 none CN(CC(=O)NC(N)=O)C[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 10, 5, 1, 11, 8, 1, 8, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 50, 50, 50, 28, 50, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 27, 27, 50, 50, 28, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 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, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479733664 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479733664 Building ZINC001479867114 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479867114 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/491 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 44, 50, 39, 22, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 40, 40, 50, 50, 50, 50, 50, 44, 44, 21, 22, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/492 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/492' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 50, 50, 50, 45, 50, 38, 24, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 39, 39, 50, 50, 50, 50, 50, 45, 45, 24, 23, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/493 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/493' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 44, 50, 39, 22, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 40, 40, 50, 50, 50, 50, 50, 44, 44, 21, 22, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/494 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/494' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 50, 50, 50, 45, 50, 38, 24, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 39, 39, 50, 50, 50, 50, 50, 45, 45, 24, 23, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479867114 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 Building ZINC001479867114 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479867114 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 491) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 44, 50, 39, 22, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 40, 40, 50, 50, 50, 50, 50, 44, 44, 21, 22, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 492) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 50, 50, 50, 45, 50, 38, 24, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 39, 39, 50, 50, 50, 50, 50, 45, 45, 24, 23, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 493) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 44, 50, 39, 22, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 40, 40, 50, 50, 50, 50, 50, 44, 44, 21, 22, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 494) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 50, 50, 50, 45, 50, 38, 24, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 39, 39, 50, 50, 50, 50, 50, 45, 45, 24, 23, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479867114 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 Building ZINC001479867114 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479867114 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 491) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 44, 50, 39, 22, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 40, 40, 50, 50, 50, 50, 50, 44, 44, 21, 22, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 492) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 50, 50, 50, 45, 50, 38, 24, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 39, 39, 50, 50, 50, 50, 50, 45, 45, 24, 23, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 493) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 44, 50, 39, 22, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 40, 40, 50, 50, 50, 50, 50, 44, 44, 21, 22, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 494) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 50, 50, 50, 45, 50, 38, 24, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 39, 39, 50, 50, 50, 50, 50, 45, 45, 24, 23, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479867114 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 Building ZINC001479867114 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479867114 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 491) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 44, 50, 39, 22, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 40, 40, 50, 50, 50, 50, 50, 44, 44, 21, 22, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 492) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 50, 50, 50, 45, 50, 38, 24, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 39, 39, 50, 50, 50, 50, 50, 45, 45, 24, 23, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 493) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 44, 50, 39, 22, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 40, 40, 50, 50, 50, 50, 50, 44, 44, 21, 22, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 494) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001479867114.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479867114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001479867114 none CNC(=O)NC(=O)CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 50, 50, 50, 45, 50, 38, 24, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 39, 39, 50, 50, 50, 50, 50, 45, 45, 24, 23, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479867114 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479867114 Building ZINC001479885593 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479885593 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/495 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 16, 37, 50, 50, 50, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 16, 16, 37, 48, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/496 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/496' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 12, 17, 40, 50, 50, 50, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 17, 17, 40, 49, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/497 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/497' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 16, 37, 50, 50, 50, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 16, 16, 37, 48, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/498 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/498' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 12, 17, 40, 50, 50, 50, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 17, 17, 40, 49, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479885593 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 Building ZINC001479885593 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479885593 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 495) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 16, 37, 50, 50, 50, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 16, 16, 37, 48, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 496) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 12, 17, 40, 50, 50, 50, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 17, 17, 40, 49, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 497) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 16, 37, 50, 50, 50, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 16, 16, 37, 48, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 498) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 12, 17, 40, 50, 50, 50, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 17, 17, 40, 49, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479885593 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 Building ZINC001479885593 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479885593 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 495) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 16, 37, 50, 50, 50, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 16, 16, 37, 48, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 496) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 12, 17, 40, 50, 50, 50, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 17, 17, 40, 49, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 497) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 16, 37, 50, 50, 50, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 16, 16, 37, 48, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 498) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 12, 17, 40, 50, 50, 50, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 17, 17, 40, 49, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479885593 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 Building ZINC001479885593 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479885593 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 495) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 16, 37, 50, 50, 50, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 16, 16, 37, 48, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 496) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 12, 17, 40, 50, 50, 50, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 17, 17, 40, 49, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 497) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 16, 37, 50, 50, 50, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 16, 16, 37, 48, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 498) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1) `ZINC001479885593.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479885593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001479885593 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CC[N@@](CCNS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 12, 17, 40, 50, 50, 50, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 17, 17, 40, 49, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479885593 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479885593 Building ZINC001479917919 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479917919 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/499 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 42, 42, 42, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 49, 49, 49, 49, 42, 42, 42, 42, 21, 22, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/500 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/500' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 42, 42, 42, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 49, 49, 49, 49, 42, 42, 42, 42, 21, 22, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/501 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/501' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 48, 41, 41, 41, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50, 48, 48, 48, 48, 41, 41, 41, 41, 22, 21, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/502 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/502' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 48, 41, 41, 41, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50, 48, 48, 48, 48, 41, 41, 41, 41, 22, 21, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479917919 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 Building ZINC001479917919 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479917919 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 499) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 42, 42, 42, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 49, 49, 49, 49, 42, 42, 42, 42, 21, 22, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 500) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 42, 42, 42, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 49, 49, 49, 49, 42, 42, 42, 42, 21, 22, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 501) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 48, 41, 41, 41, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50, 48, 48, 48, 48, 41, 41, 41, 41, 22, 21, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 502) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 48, 41, 41, 41, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50, 48, 48, 48, 48, 41, 41, 41, 41, 22, 21, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479917919 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 Building ZINC001479917919 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479917919 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 499) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 42, 42, 42, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 49, 49, 49, 49, 42, 42, 42, 42, 21, 22, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 500) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 42, 42, 42, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 49, 49, 49, 49, 42, 42, 42, 42, 21, 22, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 501) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 48, 41, 41, 41, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50, 48, 48, 48, 48, 41, 41, 41, 41, 22, 21, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 502) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 48, 41, 41, 41, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50, 48, 48, 48, 48, 41, 41, 41, 41, 22, 21, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479917919 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 Building ZINC001479917919 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479917919 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 499) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 42, 42, 42, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 49, 49, 49, 49, 42, 42, 42, 42, 21, 22, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 500) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@@](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 42, 42, 42, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 49, 49, 49, 49, 42, 42, 42, 42, 21, 22, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 501) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 48, 41, 41, 41, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50, 48, 48, 48, 48, 41, 41, 41, 41, 22, 21, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 502) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC[N@]1CC[N@@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479917919.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479917919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479917919 none CCOCC[N@]1CC[N@@](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 48, 41, 41, 41, 41, 22, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50, 48, 48, 48, 48, 41, 41, 41, 41, 22, 21, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41] 50 rigid atoms, others: [48, 45, 50, 51, 49, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479917919 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479917919 Building ZINC001479928682 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479928682 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/503 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 15, 15, 20, 36, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 10, 15, 15, 15, 15, 36, 36, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/504 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/504' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 10, 10, 10, 14, 14, 20, 37, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 10, 10, 10, 10, 14, 14, 14, 14, 37, 37, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/505 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/505' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 15, 15, 20, 36, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 10, 15, 15, 15, 15, 36, 36, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/506 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/506' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 10, 10, 10, 14, 14, 20, 37, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 10, 10, 10, 10, 14, 14, 14, 14, 37, 37, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479928682 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 Building ZINC001479928682 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479928682 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 503) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 15, 15, 20, 36, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 10, 15, 15, 15, 15, 36, 36, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 504) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 10, 10, 10, 14, 14, 20, 37, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 10, 10, 10, 10, 14, 14, 14, 14, 37, 37, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 505) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 15, 15, 20, 36, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 10, 15, 15, 15, 15, 36, 36, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 506) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 10, 10, 10, 14, 14, 20, 37, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 10, 10, 10, 10, 14, 14, 14, 14, 37, 37, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479928682 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 Building ZINC001479928682 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479928682 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 503) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 15, 15, 20, 36, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 10, 15, 15, 15, 15, 36, 36, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 504) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 10, 10, 10, 14, 14, 20, 37, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 10, 10, 10, 10, 14, 14, 14, 14, 37, 37, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 505) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 15, 15, 20, 36, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 10, 15, 15, 15, 15, 36, 36, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 506) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 10, 10, 10, 14, 14, 20, 37, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 10, 10, 10, 10, 14, 14, 14, 14, 37, 37, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479928682 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 Building ZINC001479928682 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479928682 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 503) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 15, 15, 20, 36, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 10, 15, 15, 15, 15, 36, 36, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 504) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 10, 10, 10, 14, 14, 20, 37, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 10, 10, 10, 10, 14, 14, 14, 14, 37, 37, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 505) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 15, 15, 20, 36, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 10, 15, 15, 15, 15, 36, 36, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 506) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](CCOCC2CC2)CC1) `ZINC001479928682.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479928682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001479928682 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](CCOCC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 10, 10, 10, 14, 14, 20, 37, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 10, 10, 10, 10, 14, 14, 14, 14, 37, 37, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479928682 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928682 Building ZINC001479928826 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479928826 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/507 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 43, 43, 42, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 43, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/508 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/508' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 42, 42, 40, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 42, 42, 42, 42, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/509 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/509' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 43, 43, 41, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 43, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/510 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/510' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 43, 43, 41, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 43, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479928826 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 Building ZINC001479928826 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479928826 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 507) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 43, 43, 42, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 43, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 508) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 42, 42, 40, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 42, 42, 42, 42, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 509) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 43, 43, 41, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 43, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 510) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 43, 43, 41, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 43, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479928826 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 Building ZINC001479928826 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479928826 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 507) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 43, 43, 42, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 43, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 508) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 42, 42, 40, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 42, 42, 42, 42, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 509) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 43, 43, 41, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 43, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 510) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 43, 43, 41, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 43, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479928826 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 Building ZINC001479928826 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479928826 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 507) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 43, 43, 42, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 43, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 508) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 42, 42, 40, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 42, 42, 42, 42, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 509) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 43, 43, 41, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 43, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 510) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479928826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479928826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479928826 none Cc1nonc1C[N@]1CC[N@@](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 43, 43, 41, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 43, 43, 43, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479928826 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479928826 Building ZINC001479929099 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479929099 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/511 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 36, 36, 36, 36, 49, 50, 50, 50, 50, 36, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 36, 36, 36, 49, 49, 50, 36, 36, 36, 34] 50 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, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/512 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/512' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 37, 37, 37, 37, 49, 50, 50, 50, 50, 37, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 37, 37, 37, 37, 49, 49, 50, 37, 37, 37, 34] 50 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, 43, 44, 45, 46, 47]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/513 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/513' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 36, 36, 36, 36, 49, 50, 50, 50, 50, 36, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 36, 36, 36, 49, 49, 50, 36, 36, 36, 34] 50 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, 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/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/514 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/514' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 36, 36, 36, 36, 49, 50, 50, 50, 50, 36, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 36, 36, 36, 49, 49, 50, 36, 36, 34, 36] 50 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, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479929099 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 Building ZINC001479929099 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479929099 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 511) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 36, 36, 36, 36, 49, 50, 50, 50, 50, 36, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 36, 36, 36, 49, 49, 50, 36, 36, 36, 34] 50 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, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 512) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 37, 37, 37, 37, 49, 50, 50, 50, 50, 37, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 37, 37, 37, 37, 49, 49, 50, 37, 37, 37, 34] 50 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, 43, 44, 45, 46, 47]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 513) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 36, 36, 36, 36, 49, 50, 50, 50, 50, 36, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 36, 36, 36, 49, 49, 50, 36, 36, 36, 34] 50 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, 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/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 514) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 36, 36, 36, 36, 49, 50, 50, 50, 50, 36, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 36, 36, 36, 49, 49, 50, 36, 36, 34, 36] 50 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, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479929099 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 Building ZINC001479929099 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479929099 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 511) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 36, 36, 36, 36, 49, 50, 50, 50, 50, 36, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 36, 36, 36, 49, 49, 50, 36, 36, 36, 34] 50 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, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 512) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 37, 37, 37, 37, 49, 50, 50, 50, 50, 37, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 37, 37, 37, 37, 49, 49, 50, 37, 37, 37, 34] 50 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, 43, 44, 45, 46, 47]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 513) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 36, 36, 36, 36, 49, 50, 50, 50, 50, 36, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 36, 36, 36, 49, 49, 50, 36, 36, 36, 34] 50 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, 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/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 514) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 36, 36, 36, 36, 49, 50, 50, 50, 50, 36, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 36, 36, 36, 49, 49, 50, 36, 36, 34, 36] 50 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, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479929099 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 Building ZINC001479929099 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479929099 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 511) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 36, 36, 36, 36, 49, 50, 50, 50, 50, 36, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 36, 36, 36, 49, 49, 50, 36, 36, 36, 34] 50 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, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 512) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 37, 37, 37, 37, 49, 50, 50, 50, 50, 37, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 37, 37, 37, 37, 49, 49, 50, 37, 37, 37, 34] 50 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, 43, 44, 45, 46, 47]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 513) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 36, 36, 36, 36, 49, 50, 50, 50, 50, 36, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 36, 36, 36, 49, 49, 50, 36, 36, 36, 34] 50 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, 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/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 514) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](Cc2nncs2)CC1) `ZINC001479929099.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479929099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929099 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2nncs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 8, 8, 1, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 36, 36, 36, 36, 49, 50, 50, 50, 50, 36, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 36, 36, 36, 36, 49, 49, 50, 36, 36, 34, 36] 50 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, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479929099 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929099 Building ZINC001479929142 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479929142 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/515 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 24, 24, 24, 24, 28, 50, 50, 50, 50, 24, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 24, 24, 24, 24, 28, 28, 50, 24, 24, 24, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/516 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 24, 24, 24, 24, 28, 50, 50, 50, 50, 24, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 24, 24, 24, 24, 28, 28, 50, 24, 24, 23, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/517 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/517' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 23, 23, 23, 23, 27, 50, 50, 50, 50, 23, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 23, 23, 23, 23, 27, 27, 50, 23, 23, 23, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/518 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/518' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 24, 24, 24, 24, 28, 50, 50, 50, 50, 24, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 24, 24, 24, 24, 28, 28, 50, 24, 24, 24, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479929142 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 Building ZINC001479929142 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479929142 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 515) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 24, 24, 24, 24, 28, 50, 50, 50, 50, 24, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 24, 24, 24, 24, 28, 28, 50, 24, 24, 24, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 516) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 24, 24, 24, 24, 28, 50, 50, 50, 50, 24, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 24, 24, 24, 24, 28, 28, 50, 24, 24, 23, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 517) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 23, 23, 23, 23, 27, 50, 50, 50, 50, 23, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 23, 23, 23, 23, 27, 27, 50, 23, 23, 23, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 518) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 24, 24, 24, 24, 28, 50, 50, 50, 50, 24, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 24, 24, 24, 24, 28, 28, 50, 24, 24, 24, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479929142 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 Building ZINC001479929142 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479929142 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 515) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 24, 24, 24, 24, 28, 50, 50, 50, 50, 24, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 24, 24, 24, 24, 28, 28, 50, 24, 24, 24, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 516) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 24, 24, 24, 24, 28, 50, 50, 50, 50, 24, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 24, 24, 24, 24, 28, 28, 50, 24, 24, 23, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 517) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 23, 23, 23, 23, 27, 50, 50, 50, 50, 23, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 23, 23, 23, 23, 27, 27, 50, 23, 23, 23, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 518) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 24, 24, 24, 24, 28, 50, 50, 50, 50, 24, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 24, 24, 24, 24, 28, 28, 50, 24, 24, 24, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479929142 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 Building ZINC001479929142 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479929142 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 515) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 24, 24, 24, 24, 28, 50, 50, 50, 50, 24, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 24, 24, 24, 24, 28, 28, 50, 24, 24, 24, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 516) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 24, 24, 24, 24, 28, 50, 50, 50, 50, 24, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 24, 24, 24, 24, 28, 28, 50, 24, 24, 23, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 517) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 23, 23, 23, 23, 27, 50, 50, 50, 50, 23, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 23, 23, 23, 23, 27, 27, 50, 23, 23, 23, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 518) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCC[N@]1CC[N@@](Cc2cnns2)CC1) `ZINC001479929142.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479929142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001479929142 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC[N@]1CC[N@@](Cc2cnns2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 10, 5, 1, 1, 8, 8, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 24, 24, 24, 24, 28, 50, 50, 50, 50, 24, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 24, 24, 24, 24, 28, 28, 50, 24, 24, 24, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479929142 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479929142 Building ZINC001479948562 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948562 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/519 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 27, 27, 27, 27, 43, 50, 50, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 27, 27, 27, 27, 43, 43, 50, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/520 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/520' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 26, 26, 26, 26, 42, 50, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 26, 26, 26, 26, 42, 42, 50, 50, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/521 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/521' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 27, 27, 27, 27, 43, 50, 50, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 27, 27, 27, 27, 43, 43, 50, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/522 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/522' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 26, 26, 26, 26, 42, 50, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 26, 26, 26, 26, 42, 42, 50, 50, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948562 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 Building ZINC001479948562 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948562 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 519) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 27, 27, 27, 27, 43, 50, 50, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 27, 27, 27, 27, 43, 43, 50, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 520) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 26, 26, 26, 26, 42, 50, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 26, 26, 26, 26, 42, 42, 50, 50, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 521) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 27, 27, 27, 27, 43, 50, 50, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 27, 27, 27, 27, 43, 43, 50, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 522) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 26, 26, 26, 26, 42, 50, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 26, 26, 26, 26, 42, 42, 50, 50, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948562 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 Building ZINC001479948562 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948562 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 519) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 27, 27, 27, 27, 43, 50, 50, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 27, 27, 27, 27, 43, 43, 50, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 520) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 26, 26, 26, 26, 42, 50, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 26, 26, 26, 26, 42, 42, 50, 50, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 521) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 27, 27, 27, 27, 43, 50, 50, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 27, 27, 27, 27, 43, 43, 50, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 522) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 26, 26, 26, 26, 42, 50, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 26, 26, 26, 26, 42, 42, 50, 50, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948562 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 Building ZINC001479948562 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948562 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 519) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 27, 27, 27, 27, 43, 50, 50, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 27, 27, 27, 27, 43, 43, 50, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 520) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 26, 26, 26, 26, 42, 50, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 26, 26, 26, 26, 42, 42, 50, 50, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 521) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 27, 27, 27, 27, 43, 50, 50, 50, 50, 50, 50, 50, 50, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 27, 27, 27, 27, 43, 43, 50, 50, 50, 50, 50, 50, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 522) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948562.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948562 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 24, 26, 26, 26, 26, 42, 50, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 26, 26, 26, 26, 42, 42, 50, 50, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948562 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948562 Building ZINC001479948566 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948566 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/523 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 20, 23, 23, 23, 23, 39, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 39, 39, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/524 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 19, 22, 22, 22, 22, 40, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 40, 40, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/525 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/525' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 20, 23, 23, 23, 23, 39, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 39, 39, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/526 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/526' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 19, 22, 22, 22, 22, 40, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 40, 40, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948566 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 Building ZINC001479948566 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948566 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 523) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 20, 23, 23, 23, 23, 39, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 39, 39, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 524) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 19, 22, 22, 22, 22, 40, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 40, 40, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 525) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 20, 23, 23, 23, 23, 39, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 39, 39, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 526) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 19, 22, 22, 22, 22, 40, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 40, 40, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948566 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 Building ZINC001479948566 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948566 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 523) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 20, 23, 23, 23, 23, 39, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 39, 39, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 524) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 19, 22, 22, 22, 22, 40, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 40, 40, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 525) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 20, 23, 23, 23, 23, 39, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 39, 39, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 526) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 19, 22, 22, 22, 22, 40, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 40, 40, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948566 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 Building ZINC001479948566 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948566 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 523) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 20, 23, 23, 23, 23, 39, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 39, 39, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 524) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 19, 22, 22, 22, 22, 40, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 40, 40, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 525) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 20, 23, 23, 23, 23, 39, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 39, 39, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 526) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1) `ZINC001479948566.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001479948566 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(Cc2nnc3n2CCOC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 19, 22, 22, 22, 22, 40, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 40, 40, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948566 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948566 Building ZINC001479948780 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948780 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/527 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 50, 25, 25, 25, 25, 7, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 50, 44, 44, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/528 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/528' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 50, 25, 25, 25, 25, 7, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 50, 44, 44, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/529 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/529' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 50, 21, 21, 21, 21, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/530 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/530' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 50, 21, 21, 21, 21, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948780 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 Building ZINC001479948780 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948780 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 527) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 50, 25, 25, 25, 25, 7, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 50, 44, 44, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 528) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 50, 25, 25, 25, 25, 7, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 50, 44, 44, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 529) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 50, 21, 21, 21, 21, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 530) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 50, 21, 21, 21, 21, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948780 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 Building ZINC001479948780 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948780 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 527) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 50, 25, 25, 25, 25, 7, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 50, 44, 44, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 528) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 50, 25, 25, 25, 25, 7, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 50, 44, 44, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 529) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 50, 21, 21, 21, 21, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 530) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 50, 21, 21, 21, 21, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948780 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 Building ZINC001479948780 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948780 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 527) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 50, 25, 25, 25, 25, 7, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 50, 44, 44, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 528) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 50, 25, 25, 25, 25, 7, 22, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 50, 44, 44, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 529) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 50, 21, 21, 21, 21, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 530) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948780.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948780 none Cc1cc(NC(=O)CN2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 50, 21, 21, 21, 21, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948780 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948780 Building ZINC001479948781 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948781 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/531 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 21, 21, 21, 21, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/532 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 21, 21, 21, 21, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/533 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/533' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 50, 22, 22, 22, 22, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 42, 42, 22, 22, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/534 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/534' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 50, 22, 22, 22, 22, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 42, 42, 22, 22, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948781 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 Building ZINC001479948781 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948781 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 531) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 21, 21, 21, 21, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 532) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 21, 21, 21, 21, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 533) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 50, 22, 22, 22, 22, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 42, 42, 22, 22, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 534) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 50, 22, 22, 22, 22, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 42, 42, 22, 22, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948781 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 Building ZINC001479948781 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948781 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 531) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 21, 21, 21, 21, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 532) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 21, 21, 21, 21, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 533) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 50, 22, 22, 22, 22, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 42, 42, 22, 22, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 534) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 50, 22, 22, 22, 22, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 42, 42, 22, 22, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948781 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 Building ZINC001479948781 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479948781 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 531) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 21, 21, 21, 21, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 532) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 21, 21, 21, 21, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 533) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 50, 22, 22, 22, 22, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 42, 42, 22, 22, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 534) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001479948781.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479948781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001479948781 none Cc1cc(NC(=O)CN2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 50, 22, 22, 22, 22, 6, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 42, 42, 22, 22, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479948781 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479948781 Building ZINC001479976634 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479976634 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/535 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 27, 27, 27, 27, 27, 27, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 45, 45, 27, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/536 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/537 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/537' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 27, 27, 27, 27, 27, 27, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 45, 45, 27, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/538 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/538' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479976634 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 Building ZINC001479976634 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479976634 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 535) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 27, 27, 27, 27, 27, 27, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 45, 45, 27, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 536) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 537) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 27, 27, 27, 27, 27, 27, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 45, 45, 27, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 538) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479976634 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 Building ZINC001479976634 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479976634 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 535) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 27, 27, 27, 27, 27, 27, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 45, 45, 27, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 536) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 537) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 27, 27, 27, 27, 27, 27, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 45, 45, 27, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 538) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479976634 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 Building ZINC001479976634 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479976634 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 535) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 27, 27, 27, 27, 27, 27, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 45, 45, 27, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 536) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 537) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 27, 27, 27, 27, 27, 27, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 45, 45, 27, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 538) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976634.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479976634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976634 none Cn1cnnc1CN1CCC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479976634 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976634 Building ZINC001479976637 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479976637 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/539 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/540 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/540' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 28, 28, 28, 28, 28, 27, 2, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 45, 45, 28, 28, 28, 28, 27, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/541 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/541' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/542 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/542' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 28, 28, 28, 28, 28, 27, 2, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 45, 45, 28, 28, 28, 28, 27, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479976637 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 Building ZINC001479976637 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479976637 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 539) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 540) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 28, 28, 28, 28, 28, 27, 2, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 45, 45, 28, 28, 28, 28, 27, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 541) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 542) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 28, 28, 28, 28, 28, 27, 2, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 45, 45, 28, 28, 28, 28, 27, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479976637 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 Building ZINC001479976637 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479976637 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 539) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 540) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 28, 28, 28, 28, 28, 27, 2, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 45, 45, 28, 28, 28, 28, 27, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 541) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 542) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 28, 28, 28, 28, 28, 27, 2, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 45, 45, 28, 28, 28, 28, 27, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479976637 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 Building ZINC001479976637 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479976637 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 539) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 540) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 28, 28, 28, 28, 28, 27, 2, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 45, 45, 28, 28, 28, 28, 27, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 541) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 25, 25, 25, 25, 25, 25, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 40, 40, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 542) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001479976637.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479976637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001479976637 none Cn1cnnc1CN1CCC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 28, 28, 28, 28, 28, 27, 2, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 45, 45, 28, 28, 28, 28, 27, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001479976637 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001479976637 Building ZINC001480073760 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480073760 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/543 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 17, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 17, 17, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/544 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/544' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 17, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 17, 17, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/545 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/545' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/546 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/546' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480073760 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 Building ZINC001480073760 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480073760 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 543) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 17, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 17, 17, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 544) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 17, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 17, 17, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 545) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 546) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480073760 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 Building ZINC001480073760 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480073760 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 543) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 17, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 17, 17, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 544) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 17, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 17, 17, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 545) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 546) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480073760 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 Building ZINC001480073760 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480073760 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 543) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 17, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 17, 17, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 544) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 17, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 17, 17, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 545) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 546) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073760.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480073760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073760 none CCNC(=O)CN(C)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480073760 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073760 Building ZINC001480073761 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480073761 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/547 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/548 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/548' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/549 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/549' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/550 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/550' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480073761 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 Building ZINC001480073761 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480073761 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 547) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 548) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 549) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 550) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480073761 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 Building ZINC001480073761 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480073761 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 547) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 548) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 549) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 550) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480073761 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 Building ZINC001480073761 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480073761 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 547) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 548) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 30, 35, 20, 18, 20, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 35, 30, 30, 20, 20, 20, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 549) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 550) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480073761.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480073761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480073761 none CCNC(=O)CN(C)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 31, 29, 29, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480073761 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480073761 Building ZINC001480107146 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480107146 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/551 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)[C@@H](C)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480107146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480107146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480107146 none COCCCNC(=O)[C@@H](C)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 29, 15, 15, 9, 15, 7, 9, 9, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 48, 36, 36, 29, 29, 15, 9, 9, 9, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/552 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/552' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)[C@@H](C)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480107146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480107146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480107146 none COCCCNC(=O)[C@@H](C)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 24, 10, 10, 8, 10, 7, 8, 8, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 48, 48, 33, 33, 24, 24, 10, 8, 8, 8, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480107146 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146 Building ZINC001480107146 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480107146 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 551) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)[C@@H](C)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480107146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480107146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480107146 none COCCCNC(=O)[C@@H](C)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 29, 15, 15, 9, 15, 7, 9, 9, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 48, 36, 36, 29, 29, 15, 9, 9, 9, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 552) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)[C@@H](C)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480107146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480107146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480107146 none COCCCNC(=O)[C@@H](C)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 24, 10, 10, 8, 10, 7, 8, 8, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 48, 48, 33, 33, 24, 24, 10, 8, 8, 8, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480107146 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107146 Building ZINC001480107147 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480107147 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/553 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)[C@H](C)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480107147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480107147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480107147 none COCCCNC(=O)[C@H](C)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 32, 16, 16, 13, 16, 9, 13, 13, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 49, 49, 37, 37, 32, 32, 16, 13, 13, 13, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/554 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/554' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)[C@H](C)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480107147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480107147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480107147 none COCCCNC(=O)[C@H](C)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 27, 13, 13, 11, 13, 8, 11, 11, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 49, 49, 36, 36, 27, 27, 13, 11, 11, 11, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480107147 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147 Building ZINC001480107147 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480107147 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 553) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)[C@H](C)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480107147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480107147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480107147 none COCCCNC(=O)[C@H](C)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 32, 16, 16, 13, 16, 9, 13, 13, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 49, 49, 37, 37, 32, 32, 16, 13, 13, 13, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 554) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)[C@H](C)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480107147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480107147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480107147 none COCCCNC(=O)[C@H](C)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 27, 13, 13, 11, 13, 8, 11, 11, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 49, 49, 36, 36, 27, 27, 13, 11, 11, 11, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480107147 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480107147 Building ZINC001480130753 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480130753 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/555 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1nnc(CN[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001480130753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480130753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480130753 none CC(C)(C)n1nnc(CN[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 38, 20, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/556 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/556' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1nnc(CN[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001480130753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480130753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480130753 none CC(C)(C)n1nnc(CN[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 38, 20, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480130753 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753 Building ZINC001480130753 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480130753 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 555) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1nnc(CN[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001480130753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480130753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480130753 none CC(C)(C)n1nnc(CN[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 38, 20, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 556) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1nnc(CN[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001480130753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480130753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480130753 none CC(C)(C)n1nnc(CN[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 38, 20, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480130753 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480130753 Building ZINC001480131129 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480131129 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/557 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)NCCN[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480131129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480131129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001480131129 none CC(C)NC(=O)NCCN[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 38, 24, 13, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 38, 38, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/558 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/558' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)NCCN[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480131129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480131129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001480131129 none CC(C)NC(=O)NCCN[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 49, 41, 38, 25, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 49, 41, 41, 38, 38, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480131129 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129 Building ZINC001480131129 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480131129 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 557) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)NCCN[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480131129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480131129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001480131129 none CC(C)NC(=O)NCCN[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 38, 24, 13, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 38, 38, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 558) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)NCCN[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480131129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480131129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001480131129 none CC(C)NC(=O)NCCN[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 49, 41, 38, 25, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 49, 41, 41, 38, 38, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480131129 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131129 Building ZINC001480131803 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480131803 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/559 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001480131803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480131803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001480131803 none Cc1cc(NC(=O)CN[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'H', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 50, 24, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 48, 48, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/560 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/560' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001480131803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480131803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001480131803 none Cc1cc(NC(=O)CN[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'H', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 50, 23, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 48, 48, 23, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480131803 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803 Building ZINC001480131803 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480131803 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 559) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001480131803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480131803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001480131803 none Cc1cc(NC(=O)CN[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'H', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 50, 24, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 48, 48, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 560) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001480131803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480131803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001480131803 none Cc1cc(NC(=O)CN[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'H', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 50, 23, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 48, 48, 23, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480131803 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480131803 Building ZINC001480177795 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177795 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/561 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/562 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/563 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/563' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/564 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/564' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/565 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/565' -> `4.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/566 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/566' -> `5.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/567 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/567' -> `6.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/568 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/568' -> `7.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177795 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 Building ZINC001480177795 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177795 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 561) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 562) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 563) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 564) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 565) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 566) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 567) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 568) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177795 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 Building ZINC001480177795 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177795 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 561) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 562) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 563) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 564) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 565) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 566) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 567) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 568) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177795 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 Building ZINC001480177795 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177795 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 561) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 562) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 563) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 564) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 565) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 566) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 567) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 568) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177795 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 Building ZINC001480177795 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177795 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 561) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 562) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 563) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 564) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 565) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 566) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 567) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 568) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177795 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 Building ZINC001480177795 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177795 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 561) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 562) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 563) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 564) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 565) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 566) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 567) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 568) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177795 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 Building ZINC001480177795 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177795 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 561) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 562) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 563) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 564) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 565) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 566) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 567) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 568) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177795 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 Building ZINC001480177795 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177795 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 561) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 562) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 563) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 564) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 565) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 566) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 567) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 568) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O) `ZINC001480177795.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177795 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177795 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177795 Building ZINC001480177796 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177796 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/569 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/570 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/571 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/571' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/572 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/572' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/573 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/573' -> `4.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/574 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/574' -> `5.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/575 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/575' -> `6.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/576 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/576' -> `7.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177796 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 Building ZINC001480177796 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177796 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 569) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 570) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 571) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 572) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 573) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 574) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 575) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 576) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177796 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 Building ZINC001480177796 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177796 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 569) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 570) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 571) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 572) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 573) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 574) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 575) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 576) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177796 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 Building ZINC001480177796 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177796 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 569) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 570) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 571) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 572) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 573) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 574) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 575) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 576) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177796 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 Building ZINC001480177796 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177796 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 569) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 570) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 571) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 572) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 573) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 574) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 575) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 576) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177796 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 Building ZINC001480177796 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177796 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 569) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 570) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 571) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 572) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 573) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 574) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 575) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 576) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177796 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 Building ZINC001480177796 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177796 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 569) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 570) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 571) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 572) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 573) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 574) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 575) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 576) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177796 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 Building ZINC001480177796 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001480177796 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 569) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 570) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 571) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 572) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `4' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 4 (index: 573) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 34, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `5' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 5 (index: 574) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `6' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 6 (index: 575) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `7' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 7 (index: 576) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O) `ZINC001480177796.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001480177796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480177796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H](C1)N2[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480177796 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 6: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/6.* 4: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/4.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/3.* 7: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/7.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/1.* 5: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796/5.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480177796 Building ZINC001480197555 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480197555 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/577 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NCC(=O)NCc2ccco2)C1) `ZINC001480197555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480197555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480197555 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NCC(=O)NCc2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 10, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 17, 27, 31, 31, 31, 42, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 17, 27, 27, 31, 42, 42, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/578 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/578' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NCC(=O)NCc2ccco2)C1) `ZINC001480197555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480197555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480197555 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NCC(=O)NCc2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 10, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 15, 23, 29, 29, 29, 38, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 23, 23, 29, 38, 38, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480197555 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555 Building ZINC001480197555 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480197555 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 577) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NCC(=O)NCc2ccco2)C1) `ZINC001480197555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480197555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480197555 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NCC(=O)NCc2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 10, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 17, 27, 31, 31, 31, 42, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 17, 27, 27, 31, 42, 42, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 578) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NCC(=O)NCc2ccco2)C1) `ZINC001480197555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480197555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480197555 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NCC(=O)NCc2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 10, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 15, 23, 29, 29, 29, 38, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 23, 23, 29, 38, 38, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480197555 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197555 Building ZINC001480197661 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480197661 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/579 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001480197661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480197661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480197661 none Cc1cc(NC(=O)CN[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'H', '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', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 31, 39, 17, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 44] 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, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/580 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/580' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)CN[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001480197661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480197661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480197661 none Cc1cc(NC(=O)CN[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'H', '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', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 28, 38, 17, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 44] 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, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480197661 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661 Building ZINC001480197661 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480197661 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 579) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001480197661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480197661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480197661 none Cc1cc(NC(=O)CN[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'H', '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', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 31, 39, 17, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 44] 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, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 580) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CN[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001480197661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480197661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480197661 none Cc1cc(NC(=O)CN[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'H', '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', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 10, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 28, 38, 17, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 44] 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, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480197661 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480197661 Building ZINC001480247948 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480247948 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/581 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 41, 49, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 41, 41, 49, 49, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/582 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/582' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 30, 30, 30, 30, 30, 30, 43, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 43, 43, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/583 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/583' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 41, 49, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 41, 41, 49, 49, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/584 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/584' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 30, 30, 30, 30, 30, 30, 43, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 43, 43, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480247948 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 Building ZINC001480247948 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480247948 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 581) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 41, 49, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 41, 41, 49, 49, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 582) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 30, 30, 30, 30, 30, 30, 43, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 43, 43, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 583) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 41, 49, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 41, 41, 49, 49, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 584) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 30, 30, 30, 30, 30, 30, 43, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 43, 43, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480247948 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 Building ZINC001480247948 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480247948 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 581) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 41, 49, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 41, 41, 49, 49, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 582) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 30, 30, 30, 30, 30, 30, 43, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 43, 43, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 583) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 41, 49, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 41, 41, 49, 49, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 584) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 30, 30, 30, 30, 30, 30, 43, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 43, 43, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480247948 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 Building ZINC001480247948 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480247948 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 581) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 41, 49, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 41, 41, 49, 49, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 582) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 30, 30, 30, 30, 30, 30, 43, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 43, 43, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 583) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 41, 49, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 41, 41, 49, 49, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 584) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247948.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480247948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247948 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 30, 30, 30, 30, 30, 30, 43, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 43, 43, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480247948 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247948 Building ZINC001480247949 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480247949 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/585 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 42, 42, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/586 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 29, 29, 29, 29, 29, 29, 40, 49, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 29, 29, 40, 40, 49, 49, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/587 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/587' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 42, 42, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/588 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/588' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 29, 29, 29, 29, 29, 29, 40, 49, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 29, 29, 40, 40, 49, 49, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480247949 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 Building ZINC001480247949 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480247949 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 585) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 42, 42, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 586) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 29, 29, 29, 29, 29, 29, 40, 49, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 29, 29, 40, 40, 49, 49, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 587) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 42, 42, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 588) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 29, 29, 29, 29, 29, 29, 40, 49, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 29, 29, 40, 40, 49, 49, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480247949 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 Building ZINC001480247949 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480247949 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 585) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 42, 42, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 586) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 29, 29, 29, 29, 29, 29, 40, 49, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 29, 29, 40, 40, 49, 49, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 587) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 42, 42, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 588) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 29, 29, 29, 29, 29, 29, 40, 49, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 29, 29, 40, 40, 49, 49, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480247949 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 Building ZINC001480247949 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480247949 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 585) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 42, 42, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 586) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 29, 29, 29, 29, 29, 29, 40, 49, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 29, 29, 40, 40, 49, 49, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 587) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 30, 30, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 30, 42, 42, 50, 50, 50, 50, 50, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 588) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H]1CCCN(CCN2CCNC2=O)C1) `ZINC001480247949.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480247949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480247949 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(CCN2CCNC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 29, 29, 29, 29, 29, 29, 40, 49, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 29, 29, 40, 40, 49, 49, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480247949 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480247949 Building ZINC001480275528 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480275528 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/589 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480275528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275528 none C[C@@H](NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 35, 46, 21, 8, 8, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 8, 46, 50, 50, 50, 50, 46, 46, 46, 35, 21, 21, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/590 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480275528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275528 none C[C@@H](NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 47, 23, 8, 8, 8, 8, 8, 8, 6, 2, 7, 1, 1, 1, 1, 1, 1, 8, 47, 50, 50, 50, 50, 47, 47, 47, 36, 23, 23, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480275528 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528 Building ZINC001480275528 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480275528 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 589) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/589: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480275528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275528 none C[C@@H](NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 35, 46, 21, 8, 8, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 8, 46, 50, 50, 50, 50, 46, 46, 46, 35, 21, 21, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 590) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480275528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275528 none C[C@@H](NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 47, 23, 8, 8, 8, 8, 8, 8, 6, 2, 7, 1, 1, 1, 1, 1, 1, 8, 47, 50, 50, 50, 50, 47, 47, 47, 36, 23, 23, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480275528 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275528 Building ZINC001480275529 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480275529 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/591 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480275529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275529 none C[C@@H](NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 37, 46, 20, 7, 7, 7, 7, 7, 7, 5, 2, 6, 1, 1, 1, 1, 1, 1, 7, 46, 50, 50, 50, 50, 46, 46, 46, 37, 20, 20, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/592 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480275529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275529 none C[C@@H](NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 47, 21, 9, 9, 9, 9, 9, 9, 8, 2, 9, 1, 1, 1, 1, 1, 1, 9, 47, 50, 50, 50, 50, 47, 47, 47, 36, 21, 21, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480275529 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529 Building ZINC001480275529 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480275529 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 591) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480275529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275529 none C[C@@H](NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 37, 46, 20, 7, 7, 7, 7, 7, 7, 5, 2, 6, 1, 1, 1, 1, 1, 1, 7, 46, 50, 50, 50, 50, 46, 46, 46, 37, 20, 20, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 592) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480275529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275529 none C[C@@H](NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 36, 47, 21, 9, 9, 9, 9, 9, 9, 8, 2, 9, 1, 1, 1, 1, 1, 1, 9, 47, 50, 50, 50, 50, 47, 47, 47, 36, 21, 21, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480275529 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275529 Building ZINC001480275530 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480275530 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/593 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480275530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275530 none C[C@H](NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 48, 23, 10, 10, 10, 10, 10, 10, 9, 2, 10, 1, 1, 1, 1, 1, 1, 10, 48, 50, 50, 50, 50, 48, 48, 48, 37, 23, 23, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/594 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480275530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275530 none C[C@H](NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 49, 25, 5, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 1, 1, 1, 5, 49, 50, 50, 50, 50, 49, 49, 49, 41, 25, 25, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480275530 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530 Building ZINC001480275530 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480275530 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 593) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480275530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275530 none C[C@H](NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 48, 23, 10, 10, 10, 10, 10, 10, 9, 2, 10, 1, 1, 1, 1, 1, 1, 10, 48, 50, 50, 50, 50, 48, 48, 48, 37, 23, 23, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 594) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480275530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275530 none C[C@H](NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 49, 25, 5, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 1, 1, 1, 5, 49, 50, 50, 50, 50, 49, 49, 49, 41, 25, 25, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480275530 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275530 Building ZINC001480275531 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480275531 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/595 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480275531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275531 none C[C@H](NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 35, 46, 21, 6, 6, 6, 6, 6, 6, 4, 2, 5, 1, 1, 1, 1, 1, 1, 6, 46, 50, 50, 50, 50, 46, 46, 46, 35, 21, 21, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/596 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/596' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480275531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275531 none C[C@H](NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 44, 18, 8, 8, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 8, 44, 50, 50, 50, 50, 44, 44, 44, 36, 18, 18, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480275531 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531 Building ZINC001480275531 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480275531 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 595) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480275531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275531 none C[C@H](NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 35, 46, 21, 6, 6, 6, 6, 6, 6, 4, 2, 5, 1, 1, 1, 1, 1, 1, 6, 46, 50, 50, 50, 50, 46, 46, 46, 35, 21, 21, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 596) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001480275531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480275531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480275531 none C[C@H](NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', '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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 44, 18, 8, 8, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 8, 44, 50, 50, 50, 50, 44, 44, 44, 36, 18, 18, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480275531 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480275531 Building ZINC001480276456 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480276456 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/597 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/597' -> `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](CNCCS(C)(=O)=O)C1) `ZINC001480276456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480276456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001480276456 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CNCCS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 10, 19, 29, 29, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 19, 29, 29, 29, 29, 50, 50, 50, 6, 6] 50 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/598 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/598' -> `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](CNCCS(C)(=O)=O)C1) `ZINC001480276456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480276456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001480276456 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CNCCS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 6, 10, 10, 10, 10, 10, 10, 13, 20, 34, 34, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 13, 13, 20, 34, 34, 34, 34, 50, 50, 50, 10, 10] 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, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480276456 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456 Building ZINC001480276456 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480276456 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 597) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](CNCCS(C)(=O)=O)C1) `ZINC001480276456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480276456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001480276456 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CNCCS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 10, 19, 29, 29, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 19, 29, 29, 29, 29, 50, 50, 50, 6, 6] 50 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 598) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](CNCCS(C)(=O)=O)C1) `ZINC001480276456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480276456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001480276456 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CNCCS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 6, 10, 10, 10, 10, 10, 10, 13, 20, 34, 34, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 13, 13, 20, 34, 34, 34, 34, 50, 50, 50, 10, 10] 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, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480276456 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276456 Building ZINC001480276457 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480276457 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/599 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/599' -> `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](CNCCS(C)(=O)=O)C1) `ZINC001480276457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480276457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001480276457 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CNCCS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 7, 11, 11, 11, 11, 11, 11, 14, 21, 35, 35, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 14, 14, 21, 35, 35, 35, 35, 50, 50, 50, 11, 11] 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, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/600 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/600' -> `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](CNCCS(C)(=O)=O)C1) `ZINC001480276457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480276457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001480276457 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CNCCS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 11, 19, 30, 30, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 11, 11, 19, 30, 30, 30, 30, 50, 50, 50, 6, 6] 50 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480276457 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457 Building ZINC001480276457 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480276457 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 599) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](CNCCS(C)(=O)=O)C1) `ZINC001480276457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480276457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001480276457 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CNCCS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 7, 11, 11, 11, 11, 11, 11, 14, 21, 35, 35, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 14, 14, 21, 35, 35, 35, 35, 50, 50, 50, 11, 11] 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, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 600) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](CNCCS(C)(=O)=O)C1) `ZINC001480276457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480276457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001480276457 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CNCCS(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 14, 5, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 11, 19, 30, 30, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 11, 11, 19, 30, 30, 30, 30, 50, 50, 50, 6, 6] 50 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480276457 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480276457 Building ZINC001480341812 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480341812 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/601 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480341812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341812 none C[C@@H](NC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 28, 41, 15, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 41, 50, 41, 41, 41, 28, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 41] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/602 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/602' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480341812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341812 none C[C@@H](NC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 27, 41, 16, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 41, 50, 41, 41, 41, 27, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 41] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 241 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480341812 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812 Building ZINC001480341812 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480341812 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 601) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480341812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341812 none C[C@@H](NC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 28, 41, 15, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 41, 50, 41, 41, 41, 28, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 41] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 216 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 602) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/602: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480341812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341812 none C[C@@H](NC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 27, 41, 16, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 41, 50, 41, 41, 41, 27, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 41] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 241 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480341812 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341812 Building ZINC001480341814 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480341814 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/603 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480341814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341814 none C[C@@H](NC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 26, 44, 13, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 44, 50, 50, 50, 44, 50, 44, 44, 44, 26, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 44] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/604 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480341814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341814 none C[C@@H](NC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 31, 42, 18, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 42, 42, 42, 31, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480341814 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814 Building ZINC001480341814 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480341814 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 603) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/603: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480341814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341814 none C[C@@H](NC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 26, 44, 13, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 44, 50, 50, 50, 44, 50, 44, 44, 44, 26, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 44] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 227 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 604) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480341814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341814 none C[C@@H](NC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 31, 42, 18, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 42, 42, 42, 31, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480341814 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341814 Building ZINC001480341815 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480341815 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/605 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480341815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341815 none C[C@H](NC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 23, 37, 13, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 37, 50, 37, 37, 37, 23, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 37] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/606 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480341815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341815 none C[C@H](NC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 28, 41, 14, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 41, 50, 41, 41, 41, 28, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 41] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 210 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480341815 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815 Building ZINC001480341815 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480341815 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 605) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480341815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341815 none C[C@H](NC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 23, 37, 13, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 37, 50, 37, 37, 37, 23, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 37] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 606) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480341815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341815 none C[C@H](NC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 28, 41, 14, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 41, 50, 41, 41, 41, 28, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 41] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 210 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480341815 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341815 Building ZINC001480341817 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480341817 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/607 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480341817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341817 none C[C@H](NC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 25, 42, 14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 42, 50, 42, 42, 42, 25, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 42] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/608 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/608' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480341817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341817 none C[C@H](NC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 29, 41, 18, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 41, 50, 41, 41, 41, 29, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 41] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 226 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480341817 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817 Building ZINC001480341817 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480341817 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 607) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480341817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341817 none C[C@H](NC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 25, 42, 14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 42, 50, 42, 42, 42, 25, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 42] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 608) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O) `ZINC001480341817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480341817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480341817 none C[C@H](NC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 29, 41, 18, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 41, 50, 41, 41, 41, 29, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 41] 50 rigid atoms, others: [48, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 226 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480341817 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480341817 Building ZINC001480342696 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480342696 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/609 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCS(=O)(=O)C2)CC1) `ZINC001480342696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480342696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001480342696 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 15, 15, 15, 15, 49, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/610 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/610' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCS(=O)(=O)C2)CC1) `ZINC001480342696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480342696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001480342696 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 119 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480342696 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696 Building ZINC001480342696 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480342696 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 609) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCS(=O)(=O)C2)CC1) `ZINC001480342696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480342696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001480342696 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 15, 15, 15, 15, 49, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 610) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCS(=O)(=O)C2)CC1) `ZINC001480342696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480342696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001480342696 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H]2CCCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 119 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480342696 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342696 Building ZINC001480342698 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480342698 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/611 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCS(=O)(=O)C2)CC1) `ZINC001480342698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480342698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001480342698 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 14, 14, 14, 14, 48, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 127 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/612 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCS(=O)(=O)C2)CC1) `ZINC001480342698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480342698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001480342698 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480342698 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698 Building ZINC001480342698 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480342698 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 611) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCS(=O)(=O)C2)CC1) `ZINC001480342698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480342698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001480342698 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 14, 14, 14, 14, 48, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 127 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 612) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCS(=O)(=O)C2)CC1) `ZINC001480342698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480342698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001480342698 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H]2CCCS(=O)(=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480342698 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480342698 Building ZINC001480400668 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480400668 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/613 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O) `ZINC001480400668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480400668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480400668 none C[C@@H](N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', '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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 20, 24, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 24, 50, 50, 50, 24, 50, 24, 24, 24, 20, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 24] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/614 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/614' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O) `ZINC001480400668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480400668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480400668 none C[C@@H](N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', '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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 17, 17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 37, 50, 50, 50, 37, 50, 37, 37, 37, 35, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 37] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480400668 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668 Building ZINC001480400668 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480400668 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 613) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/613: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O) `ZINC001480400668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480400668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480400668 none C[C@@H](N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', '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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 20, 24, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 24, 50, 50, 50, 24, 50, 24, 24, 24, 20, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 24] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 614) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O) `ZINC001480400668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480400668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480400668 none C[C@@H](N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', '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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 17, 17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 37, 50, 50, 50, 37, 50, 37, 37, 37, 35, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 37] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480400668 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400668 Building ZINC001480400669 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480400669 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/615 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O) `ZINC001480400669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480400669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480400669 none C[C@H](N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', '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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 18, 18, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 37, 50, 50, 50, 37, 50, 37, 37, 37, 35, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 37] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/616 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/616' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O) `ZINC001480400669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480400669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480400669 none C[C@H](N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', '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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 18, 23, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 23, 50, 50, 50, 24, 50, 23, 23, 23, 18, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 240 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480400669 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669 Building ZINC001480400669 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480400669 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 615) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O) `ZINC001480400669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480400669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480400669 none C[C@H](N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', '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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 18, 18, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 37, 50, 50, 50, 37, 50, 37, 37, 37, 35, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 37] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 616) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O) `ZINC001480400669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480400669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001480400669 none C[C@H](N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)C(=O)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', '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.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 6, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 18, 23, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 23, 50, 50, 50, 24, 50, 23, 23, 23, 18, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 240 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480400669 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480400669 Building ZINC001480437127 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480437127 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/617 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1) `ZINC001480437127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480437127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437127 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 25, 33, 47, 49, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 200 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/618 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/618' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1) `ZINC001480437127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480437127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437127 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 28, 39, 48, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480437127 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127 Building ZINC001480437127 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480437127 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 617) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1) `ZINC001480437127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480437127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437127 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 25, 33, 47, 49, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 200 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 618) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1) `ZINC001480437127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480437127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437127 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 28, 39, 48, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480437127 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437127 Building ZINC001480437128 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480437128 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/619 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1) `ZINC001480437128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480437128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437128 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 25, 32, 46, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 201 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/620 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/620' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1) `ZINC001480437128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480437128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437128 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 23, 32, 42, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480437128 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128 Building ZINC001480437128 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480437128 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 619) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1) `ZINC001480437128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480437128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437128 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 25, 32, 46, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 201 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 620) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1) `ZINC001480437128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480437128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437128 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 23, 32, 42, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480437128 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437128 Building ZINC001480437129 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480437129 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/621 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1) `ZINC001480437129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480437129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437129 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 25, 34, 44, 49, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/622 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1) `ZINC001480437129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480437129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437129 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 27, 41, 48, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480437129 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129 Building ZINC001480437129 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480437129 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 621) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1) `ZINC001480437129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480437129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437129 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 25, 34, 44, 49, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 204 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 622) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1) `ZINC001480437129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480437129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437129 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 27, 41, 48, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480437129 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437129 Building ZINC001480437130 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480437130 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/623 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1) `ZINC001480437130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480437130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437130 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 30, 36, 44, 48, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 209 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/624 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1) `ZINC001480437130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480437130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437130 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 23, 30, 41, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480437130 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130 Building ZINC001480437130 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480437130 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 623) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1) `ZINC001480437130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480437130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437130 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 30, 36, 44, 48, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 209 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 624) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1) `ZINC001480437130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480437130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001480437130 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 23, 30, 41, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480437130 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480437130 Building ZINC001480439589 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480439589 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/625 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCc1nnnn1c1ccccc1) `ZINC001480439589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480439589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480439589 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCc1nnnn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 25, 36, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 36, 36, 50, 50, 46, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/626 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/626' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCc1nnnn1c1ccccc1) `ZINC001480439589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480439589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480439589 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCc1nnnn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 30, 39, 47, 47, 47, 47, 47, 50, 50, 47, 50, 50, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 39, 39, 50, 50, 47, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480439589 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589 Building ZINC001480439589 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480439589 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 625) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)NCc1nnnn1c1ccccc1) `ZINC001480439589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480439589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480439589 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCc1nnnn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 25, 36, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 36, 36, 50, 50, 46, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 626) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)NCc1nnnn1c1ccccc1) `ZINC001480439589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480439589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480439589 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCc1nnnn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 30, 39, 47, 47, 47, 47, 47, 50, 50, 47, 50, 50, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 39, 39, 50, 50, 47, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480439589 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439589 Building ZINC001480439590 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480439590 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/627 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCc1nnnn1c1ccccc1) `ZINC001480439590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480439590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480439590 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCc1nnnn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 39, 47, 47, 47, 47, 47, 50, 50, 47, 50, 50, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 39, 39, 50, 50, 47, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/628 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCc1nnnn1c1ccccc1) `ZINC001480439590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480439590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480439590 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCc1nnnn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 25, 35, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 35, 35, 50, 50, 46, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 193 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480439590 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590 Building ZINC001480439590 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480439590 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 627) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)NCc1nnnn1c1ccccc1) `ZINC001480439590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480439590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480439590 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCc1nnnn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 31, 39, 47, 47, 47, 47, 47, 50, 50, 47, 50, 50, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 39, 39, 50, 50, 47, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 628) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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])C(C)(C)C)NCc1nnnn1c1ccccc1) `ZINC001480439590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480439590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480439590 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCc1nnnn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 25, 35, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 35, 35, 50, 50, 46, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 193 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480439590 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480439590 Building ZINC001480607507 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480607507 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/629 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/629' -> `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](C(=O)NCCNCCCF)C1) `ZINC001480607507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480607507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480607507 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)NCCNCCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 10, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 14, 25, 39, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 14, 14, 25, 39, 39, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 52, 53] set([48, 50, 51, 49, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/630 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/630' -> `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](C(=O)NCCNCCCF)C1) `ZINC001480607507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480607507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480607507 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)NCCNCCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 10, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 13, 15, 28, 42, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 13, 13, 15, 15, 28, 42, 42, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480607507 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507 Building ZINC001480607507 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480607507 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 629) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](C(=O)NCCNCCCF)C1) `ZINC001480607507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480607507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480607507 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)NCCNCCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 10, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 14, 25, 39, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 14, 14, 25, 39, 39, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 52, 53] set([48, 50, 51, 49, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 630) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](C(=O)NCCNCCCF)C1) `ZINC001480607507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480607507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480607507 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)NCCNCCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 10, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 13, 15, 28, 42, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 13, 13, 15, 15, 28, 42, 42, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480607507 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607507 Building ZINC001480607508 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480607508 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/631 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/631' -> `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](C(=O)NCCNCCCF)C1) `ZINC001480607508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480607508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480607508 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)NCCNCCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 10, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 14, 16, 28, 41, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 14, 14, 16, 16, 28, 41, 41, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/632 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/632' -> `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](C(=O)NCCNCCCF)C1) `ZINC001480607508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480607508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480607508 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)NCCNCCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 10, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 15, 26, 40, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 15, 15, 26, 40, 40, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 52, 53] set([48, 50, 51, 49, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480607508 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508 Building ZINC001480607508 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480607508 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 631) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](C(=O)NCCNCCCF)C1) `ZINC001480607508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480607508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480607508 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)NCCNCCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 10, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 14, 16, 28, 41, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 14, 14, 16, 16, 28, 41, 41, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 632) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](C(=O)NCCNCCCF)C1) `ZINC001480607508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480607508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001480607508 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)NCCNCCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 10, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 15, 26, 40, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 15, 15, 26, 40, 40, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 52, 53] set([48, 50, 51, 49, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480607508 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480607508 Building ZINC001480637272 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480637272 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/633 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)CNC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480637272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480637272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480637272 none COCCCNC(=O)CNC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 35, 26, 26, 22, 26, 11, 6, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 41, 41, 35, 35, 26, 22, 22, 11, 6, 6, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] 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, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/634 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/634' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)CNC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480637272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480637272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480637272 none COCCCNC(=O)CNC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 28, 18, 18, 17, 18, 11, 7, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 36, 36, 28, 28, 18, 17, 17, 11, 7, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] 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, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480637272 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272 Building ZINC001480637272 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480637272 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 633) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)CNC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480637272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480637272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480637272 none COCCCNC(=O)CNC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 35, 26, 26, 22, 26, 11, 6, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 41, 41, 35, 35, 26, 22, 22, 11, 6, 6, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] 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, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 634) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)CNC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480637272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480637272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480637272 none COCCCNC(=O)CNC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 28, 18, 18, 17, 18, 11, 7, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 36, 36, 28, 28, 18, 17, 17, 11, 7, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] 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, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480637272 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637272 Building ZINC001480637273 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480637273 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/635 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)CNC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480637273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480637273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480637273 none COCCCNC(=O)CNC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 27, 16, 16, 14, 16, 7, 5, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 36, 36, 27, 27, 16, 14, 14, 7, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] 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, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/636 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)CNC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480637273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480637273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480637273 none COCCCNC(=O)CNC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 29, 19, 19, 15, 19, 9, 8, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 39, 39, 29, 29, 19, 15, 15, 9, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] 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, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480637273 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273 Building ZINC001480637273 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480637273 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 635) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)CNC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480637273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480637273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480637273 none COCCCNC(=O)CNC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 27, 16, 16, 14, 16, 7, 5, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 36, 36, 27, 27, 16, 14, 14, 7, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] 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, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 636) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCNC(=O)CNC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480637273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480637273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480637273 none COCCCNC(=O)CNC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 29, 19, 19, 15, 19, 9, 8, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 39, 39, 29, 29, 19, 15, 15, 9, 8, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] 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, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480637273 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480637273 Building ZINC001480721880 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480721880 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/637 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 26, 26, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/638 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/638' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 23, 23, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 215 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/639 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/639' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 26, 26, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/640 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/640' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 23, 23, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 215 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480721880 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 Building ZINC001480721880 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480721880 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 637) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 26, 26, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 638) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 23, 23, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 215 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 639) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 26, 26, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 640) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 23, 23, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 215 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480721880 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 Building ZINC001480721880 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480721880 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 637) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 26, 26, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 638) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 23, 23, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 215 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 639) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 26, 26, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 640) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 23, 23, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 215 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480721880 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 Building ZINC001480721880 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480721880 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 637) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 26, 26, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 638) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 23, 23, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 215 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 639) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 26, 26, 26, 26, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 640) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721880.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480721880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721880 none CN(CCS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 16, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 23, 23, 23, 23, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 215 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480721880 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721880 Building ZINC001480721882 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480721882 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/641 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 18, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 29, 29, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/642 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/642' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 8, 25, 28, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 28, 28, 29, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 189 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/643 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/643' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 18, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 29, 29, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/644 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/644' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 8, 25, 28, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 28, 28, 29, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 189 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480721882 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 Building ZINC001480721882 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480721882 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 641) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 18, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 29, 29, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 642) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 8, 25, 28, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 28, 28, 29, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 189 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 643) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 18, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 29, 29, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 644) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 8, 25, 28, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 28, 28, 29, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 189 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480721882 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 Building ZINC001480721882 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480721882 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 641) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 18, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 29, 29, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 642) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 8, 25, 28, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 28, 28, 29, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 189 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 643) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 18, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 29, 29, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 644) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 8, 25, 28, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 28, 28, 29, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 189 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480721882 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 Building ZINC001480721882 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001480721882 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 641) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 18, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 29, 29, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 642) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 8, 25, 28, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 28, 28, 29, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 189 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 643) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 18, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 29, 29, 29, 29, 50, 50, 50, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 644) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001480721882.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001480721882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001480721882 none CN(CCS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 10, 5, 5, 14, 5, 11, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 8, 25, 28, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 28, 28, 29, 29, 50, 50, 50, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 189 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480721882 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480721882 Building ZINC001480753964 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480753964 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/645 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1noc(CN[C@@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001480753964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480753964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480753964 none COCc1noc(CN[C@@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', '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', '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, 12, 5, 1, 8, 12, 1, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 31, 18, 15, 13, 9, 13, 13, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 18, 18, 15, 13, 13, 13, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/646 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/646' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1noc(CN[C@@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001480753964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480753964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480753964 none COCc1noc(CN[C@@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', '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', '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, 12, 5, 1, 8, 12, 1, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 32, 16, 12, 8, 4, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 16, 16, 12, 8, 8, 8, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480753964 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964 Building ZINC001480753964 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480753964 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 645) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1noc(CN[C@@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001480753964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480753964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480753964 none COCc1noc(CN[C@@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', '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', '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, 12, 5, 1, 8, 12, 1, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 31, 18, 15, 13, 9, 13, 13, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 18, 18, 15, 13, 13, 13, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 646) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1noc(CN[C@@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001480753964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480753964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480753964 none COCc1noc(CN[C@@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', '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', '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, 12, 5, 1, 8, 12, 1, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 32, 16, 12, 8, 4, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 16, 16, 12, 8, 8, 8, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480753964 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753964 Building ZINC001480753965 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480753965 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/647 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1noc(CN[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001480753965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480753965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480753965 none COCc1noc(CN[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', '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', '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, 12, 5, 1, 8, 12, 1, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 32, 17, 12, 8, 4, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 17, 17, 12, 8, 8, 8, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/648 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/648' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1noc(CN[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001480753965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480753965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480753965 none COCc1noc(CN[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', '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', '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, 12, 5, 1, 8, 12, 1, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 31, 18, 15, 13, 9, 13, 13, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 18, 18, 15, 13, 13, 13, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480753965 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965 Building ZINC001480753965 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480753965 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 647) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1noc(CN[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001480753965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480753965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480753965 none COCc1noc(CN[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', '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', '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, 12, 5, 1, 8, 12, 1, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 32, 17, 12, 8, 4, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 17, 17, 12, 8, 8, 8, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 45, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 648) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1noc(CN[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001480753965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480753965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001480753965 none COCc1noc(CN[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', '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', '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, 12, 5, 1, 8, 12, 1, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 31, 18, 15, 13, 9, 13, 13, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 18, 18, 15, 13, 13, 13, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480753965 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480753965 Building ZINC001480754280 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480754280 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/649 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@H]1CCOC1) `ZINC001480754280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480754280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754280 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@H]1CCOC1 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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 11, 14, 14, 14, 38, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 14, 38, 38, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/650 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/650' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@H]1CCOC1) `ZINC001480754280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480754280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754280 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@H]1CCOC1 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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 9, 13, 20, 20, 20, 44, 50, 50, 50, 50, 50, 6, 6, 6, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 13, 13, 20, 41, 41, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480754280 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280 Building ZINC001480754280 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480754280 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 649) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@H]1CCOC1) `ZINC001480754280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480754280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754280 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@H]1CCOC1 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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 11, 14, 14, 14, 38, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 14, 38, 38, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 650) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@H]1CCOC1) `ZINC001480754280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480754280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754280 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@H]1CCOC1 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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 9, 13, 20, 20, 20, 44, 50, 50, 50, 50, 50, 6, 6, 6, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 13, 13, 20, 41, 41, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 207 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480754280 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754280 Building ZINC001480754281 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480754281 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/651 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@@H]1CCOC1) `ZINC001480754281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480754281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754281 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@@H]1CCOC1 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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 11, 14, 14, 14, 41, 50, 50, 50, 50, 50, 6, 6, 6, 5, 5, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 14, 38, 38, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 208 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/652 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@@H]1CCOC1) `ZINC001480754281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480754281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754281 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@@H]1CCOC1 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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 8, 16, 16, 16, 42, 50, 50, 50, 50, 50, 6, 6, 6, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 16, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480754281 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281 Building ZINC001480754281 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480754281 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 651) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@@H]1CCOC1) `ZINC001480754281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480754281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754281 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@@H]1CCOC1 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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 11, 14, 14, 14, 41, 50, 50, 50, 50, 50, 6, 6, 6, 5, 5, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 14, 38, 38, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 208 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 652) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@@H]1CCOC1) `ZINC001480754281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480754281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754281 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)NC[C@@H]1CCOC1 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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 8, 16, 16, 16, 42, 50, 50, 50, 50, 50, 6, 6, 6, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 16, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480754281 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754281 Building ZINC001480754780 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480754780 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/653 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)C1) `ZINC001480754780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480754780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754780 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 21, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 27, 35, 43, 48, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 204 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/654 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/654' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)C1) `ZINC001480754780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480754780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754780 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 13, 22, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 30, 36, 45, 49, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480754780 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780 Building ZINC001480754780 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480754780 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 653) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)C1) `ZINC001480754780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480754780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754780 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 21, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 27, 35, 43, 48, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 204 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 654) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)C1) `ZINC001480754780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480754780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754780 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 13, 22, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 30, 36, 45, 49, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480754780 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754780 Building ZINC001480754781 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480754781 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/655 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)C1) `ZINC001480754781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480754781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754781 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 21, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 29, 37, 44, 44, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/656 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)C1) `ZINC001480754781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480754781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754781 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 20, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 31, 39, 45, 45, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 205 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480754781 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781 Building ZINC001480754781 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480754781 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 655) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)C1) `ZINC001480754781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480754781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754781 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 21, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 29, 37, 44, 44, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 656) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)C1) `ZINC001480754781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480754781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754781 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 20, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 31, 39, 45, 45, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 205 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480754781 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754781 Building ZINC001480754782 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480754782 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/657 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)C1) `ZINC001480754782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480754782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754782 none C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 20, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 32, 39, 45, 49, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/658 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)C1) `ZINC001480754782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480754782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754782 none C[C@@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 34, 42, 48, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 213 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480754782 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782 Building ZINC001480754782 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480754782 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 657) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)C1) `ZINC001480754782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480754782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754782 none C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 20, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 32, 39, 45, 49, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 658) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)C1) `ZINC001480754782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480754782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754782 none C[C@@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 28, 34, 42, 48, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 213 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480754782 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754782 Building ZINC001480754783 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480754783 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/659 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)C1) `ZINC001480754783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480754783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754783 none C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 26, 36, 48, 48, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 221 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/660 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/660' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)C1) `ZINC001480754783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480754783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754783 none C[C@@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 21, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 27, 36, 43, 43, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 213 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480754783 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783 Building ZINC001480754783 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001480754783 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 659) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)C1) `ZINC001480754783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001480754783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754783 none C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 26, 36, 48, 48, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 221 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 660) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)C1) `ZINC001480754783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001480754783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001480754783 none C[C@@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NCC(=O)N1CCO[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 21, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 27, 36, 43, 43, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 213 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001480754783 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001480754783 Building ZINC001493012236 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493012236 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/661 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)c1cn(C)c(O)n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001493012236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493012236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493012236 none CCN(CCCNC(=O)c1cn(C)c(O)n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 12, 8, 1, 11, 5, 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, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 2, 4, 13, 15, 27, 47, 47, 47, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 16, 16, 27, 26, 47, 48, 48, 48, 48, 144, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/662 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/662' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)c1cn(C)c(O)n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001493012236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493012236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493012236 none CCN(CCCNC(=O)c1cn(C)c(O)n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 12, 8, 1, 11, 5, 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, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 2, 4, 13, 16, 28, 47, 47, 47, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 17, 17, 27, 28, 47, 48, 48, 48, 48, 144, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493012236 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236 Building ZINC001493012236 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493012236 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 661) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)c1cn(C)c(O)n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001493012236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493012236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493012236 none CCN(CCCNC(=O)c1cn(C)c(O)n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 12, 8, 1, 11, 5, 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, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 2, 4, 13, 15, 27, 47, 47, 47, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 16, 16, 27, 26, 47, 48, 48, 48, 48, 144, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 662) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)c1cn(C)c(O)n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001493012236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493012236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493012236 none CCN(CCCNC(=O)c1cn(C)c(O)n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 12, 8, 1, 11, 5, 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, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 2, 4, 13, 16, 28, 47, 47, 47, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 17, 17, 27, 28, 47, 48, 48, 48, 48, 144, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493012236 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493012236 Building ZINC001493025171 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493025171 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/663 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)CCc1cnn[nH]1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001493025171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493025171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493025171 none CCN(CCCNC(=O)CCc1cnn[nH]1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 1, 11, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 2, 3, 10, 10, 10, 37, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 10, 37, 37, 46, 46, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [2, 50, 49, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/664 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/664' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)CCc1cnn[nH]1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001493025171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493025171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493025171 none CCN(CCCNC(=O)CCc1cnn[nH]1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 1, 11, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 2, 3, 9, 9, 9, 35, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 9, 35, 35, 43, 43, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [2, 50, 49, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493025171 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171 Building ZINC001493025171 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493025171 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 663) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)CCc1cnn[nH]1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001493025171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493025171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493025171 none CCN(CCCNC(=O)CCc1cnn[nH]1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 1, 11, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 2, 3, 10, 10, 10, 37, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 10, 37, 37, 46, 46, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [2, 50, 49, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 664) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)CCc1cnn[nH]1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001493025171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493025171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493025171 none CCN(CCCNC(=O)CCc1cnn[nH]1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 1, 11, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 2, 3, 9, 9, 9, 35, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 9, 35, 35, 43, 43, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [2, 50, 49, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493025171 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493025171 Building ZINC001493041108 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493041108 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/665 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1ccc(O)nn1)C1CC1) `ZINC001493041108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493041108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493041108 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1ccc(O)nn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 16, 18, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 20, 20, 33, 32, 50, 50, 50, 100, 8, 8, 8, 8, 8] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 318 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/666 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/666' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1ccc(O)nn1)C1CC1) `ZINC001493041108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493041108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493041108 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1ccc(O)nn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 14, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 15, 15, 28, 27, 50, 50, 50, 100, 5, 5, 5, 5, 5] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 302 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493041108 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108 Building ZINC001493041108 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493041108 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 665) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1ccc(O)nn1)C1CC1) `ZINC001493041108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493041108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493041108 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1ccc(O)nn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 16, 18, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 20, 20, 33, 32, 50, 50, 50, 100, 8, 8, 8, 8, 8] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 318 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 666) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1ccc(O)nn1)C1CC1) `ZINC001493041108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493041108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493041108 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1ccc(O)nn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 14, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 15, 15, 28, 27, 50, 50, 50, 100, 5, 5, 5, 5, 5] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 302 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493041108 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493041108 Building ZINC001493050478 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493050478 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/667 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCC(=O)N1)C1CC1) `ZINC001493050478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493050478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493050478 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCC(=O)N1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 6, 6, 14, 40, 40, 44, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 40, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/668 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/668' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCC(=O)N1)C1CC1) `ZINC001493050478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493050478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493050478 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCC(=O)N1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 6, 12, 35, 35, 40, 50, 50, 50, 50, 50, 50, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 12, 35, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493050478 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478 Building ZINC001493050478 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493050478 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 667) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCC(=O)N1)C1CC1) `ZINC001493050478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493050478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493050478 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCC(=O)N1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 6, 6, 14, 40, 40, 44, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 40, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 668) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCC(=O)N1)C1CC1) `ZINC001493050478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493050478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493050478 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCC(=O)N1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 6, 12, 35, 35, 40, 50, 50, 50, 50, 50, 50, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 12, 35, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493050478 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493050478 Building ZINC001493053156 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493053156 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/669 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493053156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493053156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493053156 none CNC(=O)NCC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 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] 0 hydrogens need rotated 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, 41, 33, 33, 33, 32, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 50, 50, 50, 50, 50, 41, 41, 32, 30, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/670 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493053156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493053156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493053156 none CNC(=O)NCC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 30, 30, 30, 29, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 50, 37, 37, 29, 28, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493053156 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156 Building ZINC001493053156 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493053156 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 669) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493053156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493053156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493053156 none CNC(=O)NCC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 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] 0 hydrogens need rotated 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, 41, 33, 33, 33, 32, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 50, 50, 50, 50, 50, 41, 41, 32, 30, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 670) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493053156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493053156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493053156 none CNC(=O)NCC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 30, 30, 30, 29, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 50, 37, 37, 29, 28, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 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, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493053156 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053156 Building ZINC001493053162 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493053162 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/671 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1nccnc1N)C1CC1) `ZINC001493053162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493053162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493053162 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1nccnc1N)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 13, 15, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 16, 16, 27, 27, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/672 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/672' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1nccnc1N)C1CC1) `ZINC001493053162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493053162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493053162 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1nccnc1N)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 11, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 11, 11, 23, 23, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493053162 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162 Building ZINC001493053162 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493053162 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 671) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1nccnc1N)C1CC1) `ZINC001493053162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493053162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493053162 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1nccnc1N)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 13, 15, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 16, 16, 27, 27, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 672) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1nccnc1N)C1CC1) `ZINC001493053162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493053162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493053162 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)c1nccnc1N)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 11, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 11, 11, 23, 23, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493053162 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053162 Building ZINC001493053714 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493053714 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/673 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1ccnn1)C1CC1) `ZINC001493053714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493053714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493053714 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1ccnn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 12, 22, 29, 29, 29, 38, 40, 50, 50, 50, 50, 29, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 22, 22, 38, 38, 40, 40, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 228 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/674 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/674' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1ccnn1)C1CC1) `ZINC001493053714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493053714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493053714 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1ccnn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 20, 27, 27, 27, 37, 38, 49, 49, 49, 49, 27, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 13, 13, 20, 20, 37, 37, 38, 38, 49, 49, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493053714 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714 Building ZINC001493053714 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493053714 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 673) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCCN(C(=O)CCn1ccnn1)C1CC1) `ZINC001493053714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493053714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493053714 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1ccnn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 12, 22, 29, 29, 29, 38, 40, 50, 50, 50, 50, 29, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 22, 22, 38, 38, 40, 40, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 228 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 674) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCCN(C(=O)CCn1ccnn1)C1CC1) `ZINC001493053714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493053714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493053714 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1ccnn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 20, 27, 27, 27, 37, 38, 49, 49, 49, 49, 27, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 13, 13, 20, 20, 37, 37, 38, 38, 49, 49, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 206 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493053714 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493053714 Building ZINC001493054364 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493054364 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/675 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)C1(C(N)=O)CC1)C1CC1) `ZINC001493054364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493054364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493054364 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)C1(C(N)=O)CC1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 11, 16, 32, 45, 45, 50, 50, 50, 50, 50, 32, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/676 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/676' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)C1(C(N)=O)CC1)C1CC1) `ZINC001493054364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493054364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493054364 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)C1(C(N)=O)CC1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 10, 13, 28, 40, 40, 46, 49, 49, 46, 46, 28, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 13, 13, 13, 13, 49, 49, 46, 46, 46, 46, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 219 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493054364 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364 Building ZINC001493054364 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493054364 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 675) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCCN(C(=O)C1(C(N)=O)CC1)C1CC1) `ZINC001493054364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493054364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493054364 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)C1(C(N)=O)CC1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 11, 16, 32, 45, 45, 50, 50, 50, 50, 50, 32, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 676) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCCN(C(=O)C1(C(N)=O)CC1)C1CC1) `ZINC001493054364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493054364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493054364 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)C1(C(N)=O)CC1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 10, 13, 28, 40, 40, 46, 49, 49, 46, 46, 28, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 13, 13, 13, 13, 49, 49, 46, 46, 46, 46, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 219 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493054364 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493054364 Building ZINC001493065601 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493065601 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/677 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NCCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493065601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493065601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493065601 none C[C@H](NC(N)=O)C(=O)NCCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 50, 50, 50, 50, 48, 48, 24, 13, 12, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 8, 8, 50, 50, 50, 50, 50, 50, 48, 24, 24, 13, 13, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/678 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NCCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493065601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493065601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493065601 none C[C@H](NC(N)=O)C(=O)NCCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 50, 50, 50, 50, 46, 46, 25, 11, 10, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 46, 25, 25, 11, 11, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493065601 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601 Building ZINC001493065601 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493065601 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 677) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(N)=O)C(=O)NCCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493065601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493065601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493065601 none C[C@H](NC(N)=O)C(=O)NCCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 50, 50, 50, 50, 48, 48, 24, 13, 12, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 8, 8, 50, 50, 50, 50, 50, 50, 48, 24, 24, 13, 13, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 678) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(N)=O)C(=O)NCCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493065601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493065601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493065601 none C[C@H](NC(N)=O)C(=O)NCCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 50, 50, 50, 50, 46, 46, 25, 11, 10, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 46, 25, 25, 11, 11, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493065601 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493065601 Building ZINC001493066555 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493066555 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/679 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)NCCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001493066555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493066555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493066555 none Cn1cc(C(=O)NCCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 12, 11, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 27, 26, 13, 13, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 200 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/680 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/680' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)NCCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001493066555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493066555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493066555 none Cn1cc(C(=O)NCCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 11, 11, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 50, 24, 25, 12, 12, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493066555 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555 Building ZINC001493066555 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493066555 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 679) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)NCCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001493066555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493066555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493066555 none Cn1cc(C(=O)NCCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 12, 11, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 27, 26, 13, 13, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 200 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 680) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)NCCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1) `ZINC001493066555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493066555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493066555 none Cn1cc(C(=O)NCCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', '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, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 11, 11, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 50, 24, 25, 12, 12, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493066555 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493066555 Building ZINC001493096202 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493096202 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/681 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCNC1=O)C1CC1) `ZINC001493096202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493096202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493096202 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 5, 5, 13, 34, 34, 39, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 13, 34, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/682 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/682' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCNC1=O)C1CC1) `ZINC001493096202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493096202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493096202 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 10, 32, 32, 38, 50, 50, 50, 50, 50, 50, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 32, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493096202 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202 Building ZINC001493096202 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493096202 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 681) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCNC1=O)C1CC1) `ZINC001493096202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493096202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493096202 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 5, 5, 13, 34, 34, 39, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 13, 34, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 682) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCNC1=O)C1CC1) `ZINC001493096202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493096202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493096202 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)[C@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 5, 10, 32, 32, 38, 50, 50, 50, 50, 50, 50, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 32, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493096202 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493096202 Building ZINC001493126775 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493126775 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/683 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493126775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493126775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493126775 none COCCC(=O)N1CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 47, 49, 47, 47, 47, 27, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 24, 23, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/684 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/684' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493126775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493126775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493126775 none COCCC(=O)N1CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 41, 47, 41, 41, 41, 25, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 22, 23, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493126775 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775 Building ZINC001493126775 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493126775 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 683) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493126775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493126775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493126775 none COCCC(=O)N1CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 47, 49, 47, 47, 47, 27, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 24, 23, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 684) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493126775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493126775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493126775 none COCCC(=O)N1CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 41, 47, 41, 41, 41, 25, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 22, 23, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493126775 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493126775 Building ZINC001493153701 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493153701 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/685 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493153701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493153701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493153701 none CCOCCC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 16, 16, 16, 7, 5, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 40, 40, 16, 7, 7, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/686 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/686' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493153701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493153701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493153701 none CCOCCC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 42, 16, 16, 16, 8, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 49, 49, 42, 42, 16, 8, 8, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [48, 45, 50, 49, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493153701 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701 Building ZINC001493153701 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493153701 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 685) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493153701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493153701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493153701 none CCOCCC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 16, 16, 16, 7, 5, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 40, 40, 16, 7, 7, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 686) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493153701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493153701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493153701 none CCOCCC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 42, 16, 16, 16, 8, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 49, 49, 42, 42, 16, 8, 8, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [48, 45, 50, 49, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493153701 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493153701 Building ZINC001493154961 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493154961 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/687 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493154961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493154961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493154961 none CSCC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 34, 31, 34, 31, 31, 31, 15, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50, 50, 41, 41, 31, 31, 31, 31, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/688 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/688' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493154961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493154961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493154961 none CSCC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 35, 30, 35, 30, 30, 30, 15, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 50, 50, 50, 42, 42, 30, 30, 30, 30, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493154961 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961 Building ZINC001493154961 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493154961 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 687) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493154961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493154961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493154961 none CSCC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 34, 31, 34, 31, 31, 31, 15, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50, 50, 41, 41, 31, 31, 31, 31, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 688) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493154961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493154961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493154961 none CSCC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 35, 30, 35, 30, 30, 30, 15, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 50, 50, 50, 42, 42, 30, 30, 30, 30, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493154961 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493154961 Building ZINC001493155467 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493155467 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/689 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2ccon2)CC1) `ZINC001493155467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493155467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001493155467 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2ccon2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 1, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 16, 36, 36, 36, 36, 48, 48, 50, 50, 50, 50, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 14, 14, 36, 36, 36, 36, 50, 50, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/690 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/690' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2ccon2)CC1) `ZINC001493155467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493155467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001493155467 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2ccon2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 1, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 35, 35, 35, 35, 49, 49, 50, 50, 50, 50, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 35, 35, 35, 35, 50, 50, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493155467 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467 Building ZINC001493155467 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493155467 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 689) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN1CCN(C(=O)c2ccon2)CC1) `ZINC001493155467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493155467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001493155467 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2ccon2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 1, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 16, 36, 36, 36, 36, 48, 48, 50, 50, 50, 50, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 14, 14, 36, 36, 36, 36, 50, 50, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 690) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN1CCN(C(=O)c2ccon2)CC1) `ZINC001493155467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493155467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001493155467 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2ccon2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 1, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 35, 35, 35, 35, 49, 49, 50, 50, 50, 50, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 35, 35, 35, 35, 50, 50, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493155467 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155467 Building ZINC001493155609 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493155609 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/691 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC2(C)C)CC1) `ZINC001493155609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493155609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493155609 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC2(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 32, 32, 32, 32, 48, 48, 50, 50, 50, 50, 50, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 16, 16, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/692 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/692' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC2(C)C)CC1) `ZINC001493155609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493155609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493155609 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC2(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 24, 35, 35, 35, 35, 49, 49, 50, 50, 50, 50, 50, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 19, 19, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493155609 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609 Building ZINC001493155609 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493155609 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 691) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN1CCN(C(=O)[C@H]2CC2(C)C)CC1) `ZINC001493155609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493155609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493155609 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC2(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 32, 32, 32, 32, 48, 48, 50, 50, 50, 50, 50, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 16, 16, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 692) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN1CCN(C(=O)[C@H]2CC2(C)C)CC1) `ZINC001493155609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493155609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493155609 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC2(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 24, 35, 35, 35, 35, 49, 49, 50, 50, 50, 50, 50, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 19, 19, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493155609 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155609 Building ZINC001493155809 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493155809 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/693 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493155809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493155809 none CC(C)[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 50, 34, 46, 34, 34, 34, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 15, 15, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/694 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/694' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493155809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493155809 none CC(C)[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 46, 49, 49, 35, 46, 35, 35, 35, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 15, 15, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493155809 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809 Building ZINC001493155809 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493155809 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 693) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493155809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493155809 none CC(C)[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 50, 34, 46, 34, 34, 34, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 15, 15, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 694) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493155809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493155809 none CC(C)[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 46, 49, 49, 35, 46, 35, 35, 35, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 15, 15, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493155809 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155809 Building ZINC001493155811 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493155811 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/695 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493155811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493155811 none CC(C)[C@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 47, 49, 49, 35, 47, 35, 35, 35, 18, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/696 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/696' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493155811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493155811 none CC(C)[C@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 46, 49, 49, 33, 46, 33, 33, 33, 15, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493155811 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811 Building ZINC001493155811 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493155811 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 695) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493155811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493155811 none CC(C)[C@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 47, 49, 49, 35, 47, 35, 35, 35, 18, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 696) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493155811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493155811 none CC(C)[C@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 46, 49, 49, 33, 46, 33, 33, 33, 15, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493155811 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155811 Building ZINC001493155904 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493155904 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/697 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493155904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493155904 none CC[C@@H]1C[C@H]1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 50, 28, 38, 28, 28, 28, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 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/83982/xcb-8058097.54/working/building/ZINC001493155904 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/698 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/698' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493155904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493155904 none CC[C@@H]1C[C@H]1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 50, 33, 41, 33, 33, 33, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 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/83982/xcb-8058097.54/working/building/ZINC001493155904 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493155904 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904 Building ZINC001493155904 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493155904 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 697) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[C@H]1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493155904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493155904 none CC[C@@H]1C[C@H]1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 50, 28, 38, 28, 28, 28, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 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/83982/xcb-8058097.54/working/building/ZINC001493155904 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 698) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[C@H]1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493155904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493155904 none CC[C@@H]1C[C@H]1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 50, 33, 41, 33, 33, 33, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 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/83982/xcb-8058097.54/working/building/ZINC001493155904 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493155904 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155904 Building ZINC001493155907 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493155907 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/699 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493155907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493155907 none CCOCCC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 46, 44, 33, 44, 33, 33, 33, 21, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 46, 46, 46, 46, 33, 33, 33, 33, 19, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/700 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/700' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493155907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493155907 none CCOCCC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 46, 36, 46, 36, 36, 36, 21, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 49, 49, 49, 49, 36, 36, 36, 36, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493155907 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907 Building ZINC001493155907 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493155907 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 699) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493155907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493155907 none CCOCCC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 46, 44, 33, 44, 33, 33, 33, 21, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 46, 46, 46, 46, 33, 33, 33, 33, 19, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 700) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493155907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493155907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493155907 none CCOCCC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 49, 46, 36, 46, 36, 36, 36, 21, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 49, 49, 49, 49, 36, 36, 36, 36, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493155907 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493155907 Building ZINC001493156161 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493156161 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/701 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493156161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493156161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493156161 none CC(C)(C)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 147 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/702 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493156161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493156161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493156161 none CC(C)(C)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493156161 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161 Building ZINC001493156161 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493156161 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 701) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493156161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493156161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493156161 none CC(C)(C)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 147 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 702) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493156161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493156161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493156161 none CC(C)(C)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493156161 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493156161 Building ZINC001493166771 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493166771 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/703 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2C[C@H]2C2CC2)CC1) `ZINC001493166771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493166771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493166771 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2C[C@H]2C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 6, 15, 15, 15, 48, 48, 48, 48, 48, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 6, 6, 15, 48, 48, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 5, 34, 35, 7, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/704 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/704' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2C[C@H]2C2CC2)CC1) `ZINC001493166771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493166771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493166771 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2C[C@H]2C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 7, 8, 18, 18, 18, 48, 48, 48, 48, 48, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 8, 8, 18, 48, 48, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493166771 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771 Building ZINC001493166771 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493166771 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 703) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2C[C@H]2C2CC2)CC1) `ZINC001493166771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493166771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493166771 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2C[C@H]2C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 6, 15, 15, 15, 48, 48, 48, 48, 48, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 6, 6, 15, 48, 48, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 5, 34, 35, 7, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 704) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2C[C@H]2C2CC2)CC1) `ZINC001493166771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493166771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493166771 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2C[C@H]2C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 7, 8, 18, 18, 18, 48, 48, 48, 48, 48, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 8, 8, 18, 48, 48, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493166771 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493166771 Building ZINC001493180345 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493180345 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/705 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](F)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493180345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493180345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493180345 none CC(C)[C@@H](F)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 37, 46, 46, 37, 37, 13, 9, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 37, 13, 13, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/706 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/706' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](F)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493180345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493180345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493180345 none CC(C)[C@@H](F)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 37, 46, 46, 37, 37, 14, 11, 5, 5, 5, 5, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50, 50, 37, 14, 14, 11, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493180345 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345 Building ZINC001493180345 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493180345 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 705) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](F)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493180345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493180345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493180345 none CC(C)[C@@H](F)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 37, 46, 46, 37, 37, 13, 9, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 37, 13, 13, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 706) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](F)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493180345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493180345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493180345 none CC(C)[C@@H](F)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 37, 46, 46, 37, 37, 14, 11, 5, 5, 5, 5, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50, 50, 37, 14, 14, 11, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493180345 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180345 Building ZINC001493180347 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493180347 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/707 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](F)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493180347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493180347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493180347 none CC(C)[C@H](F)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 34, 43, 43, 34, 34, 14, 10, 5, 5, 5, 5, 4, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50, 50, 34, 14, 14, 10, 10, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/708 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/708' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](F)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493180347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493180347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493180347 none CC(C)[C@H](F)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 34, 44, 44, 34, 34, 13, 10, 5, 5, 5, 5, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50, 50, 34, 13, 13, 10, 10, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493180347 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347 Building ZINC001493180347 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493180347 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 707) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](F)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493180347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493180347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493180347 none CC(C)[C@H](F)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 34, 43, 43, 34, 34, 14, 10, 5, 5, 5, 5, 4, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50, 50, 34, 14, 14, 10, 10, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 708) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](F)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493180347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493180347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001493180347 none CC(C)[C@H](F)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 34, 44, 44, 34, 34, 13, 10, 5, 5, 5, 5, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50, 50, 34, 13, 13, 10, 10, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493180347 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493180347 Building ZINC001493181609 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493181609 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/709 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 19, 19, 19, 19, 11, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 28, 28, 19, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/710 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/710' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 19, 19, 19, 19, 11, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 28, 28, 19, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/711 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/711' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 25, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 25, 25, 21, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/712 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/712' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 25, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 25, 25, 21, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493181609 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 Building ZINC001493181609 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493181609 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 709) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 19, 19, 19, 19, 11, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 28, 28, 19, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 710) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 19, 19, 19, 19, 11, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 28, 28, 19, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 711) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 25, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 25, 25, 21, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 712) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 25, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 25, 25, 21, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493181609 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 Building ZINC001493181609 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493181609 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 709) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 19, 19, 19, 19, 11, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 28, 28, 19, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 710) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 19, 19, 19, 19, 11, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 28, 28, 19, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 711) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 25, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 25, 25, 21, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 712) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 25, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 25, 25, 21, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493181609 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 Building ZINC001493181609 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493181609 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 709) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 19, 19, 19, 19, 11, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 28, 28, 19, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 710) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 19, 19, 19, 19, 11, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 28, 28, 19, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 711) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 25, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 25, 25, 21, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 712) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181609.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493181609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181609 none CCCn1nnnc1CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 37, 37, 37, 37, 25, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 25, 25, 21, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493181609 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181609 Building ZINC001493181610 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493181610 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/713 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 30, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 30, 30, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/714 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/714' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 30, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 30, 30, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/715 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/715' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 20, 20, 20, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 28, 28, 20, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/716 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/716' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 20, 20, 20, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 28, 28, 20, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493181610 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 Building ZINC001493181610 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493181610 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 713) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 30, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 30, 30, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 714) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 30, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 30, 30, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 715) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 20, 20, 20, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 28, 28, 20, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 716) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 20, 20, 20, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 28, 28, 20, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493181610 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 Building ZINC001493181610 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493181610 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 713) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 30, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 30, 30, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 714) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 30, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 30, 30, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 715) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 20, 20, 20, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 28, 28, 20, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 716) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 20, 20, 20, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 28, 28, 20, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493181610 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 Building ZINC001493181610 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493181610 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 713) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 30, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 30, 30, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 714) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 39, 39, 39, 39, 30, 23, 23, 23, 23, 15, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 30, 30, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 715) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 20, 20, 20, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 28, 28, 20, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 716) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493181610.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493181610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493181610 none CCCn1nnnc1CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 38, 38, 38, 38, 28, 20, 20, 20, 20, 12, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 50, 28, 28, 20, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493181610 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493181610 Building ZINC001493246907 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493246907 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/717 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3nncn3C2)C1) `ZINC001493246907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493246907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493246907 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3nncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 20, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/718 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/718' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3nncn3C2)C1) `ZINC001493246907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493246907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493246907 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3nncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493246907 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907 Building ZINC001493246907 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493246907 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 717) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3nncn3C2)C1) `ZINC001493246907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493246907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493246907 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3nncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 20, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 718) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3nncn3C2)C1) `ZINC001493246907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493246907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493246907 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3nncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493246907 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246907 Building ZINC001493246910 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493246910 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/719 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3nncn3C2)C1) `ZINC001493246910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493246910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493246910 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3nncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/720 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/720' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3nncn3C2)C1) `ZINC001493246910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493246910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493246910 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3nncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 26, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 142 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493246910 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910 Building ZINC001493246910 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493246910 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 719) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3nncn3C2)C1) `ZINC001493246910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493246910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493246910 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3nncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 720) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3nncn3C2)C1) `ZINC001493246910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493246910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493246910 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3nncn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 26, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 142 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493246910 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493246910 Building ZINC001493247321 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247321 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/721 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493247321 none CC(=O)N(C)CCCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 50, 35, 33, 13, 10, 13, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 45, 43, 37, 37, 33, 33, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/722 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493247321 none CC(=O)N(C)CCCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 37, 35, 13, 9, 13, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 46, 44, 39, 39, 35, 35, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247321 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321 Building ZINC001493247321 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247321 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 721) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493247321 none CC(=O)N(C)CCCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 50, 35, 33, 13, 10, 13, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 45, 43, 37, 37, 33, 33, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 722) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493247321 none CC(=O)N(C)CCCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 37, 35, 13, 9, 13, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 46, 44, 39, 39, 35, 35, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247321 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247321 Building ZINC001493247325 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247325 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/723 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493247325 none CC(=O)N(C)CCCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 35, 32, 11, 10, 11, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 46, 45, 36, 36, 32, 32, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/724 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/724' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493247325 none CC(=O)N(C)CCCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 50, 38, 33, 12, 10, 12, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 47, 45, 40, 40, 33, 33, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247325 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325 Building ZINC001493247325 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247325 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 723) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493247325 none CC(=O)N(C)CCCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 50, 35, 32, 11, 10, 11, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 46, 45, 36, 36, 32, 32, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 724) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493247325 none CC(=O)N(C)CCCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 50, 38, 33, 12, 10, 12, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 47, 45, 40, 40, 33, 33, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247325 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247325 Building ZINC001493247433 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247433 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/725 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493247433 none CC(C)S(=O)(=O)CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 37, 49, 49, 12, 8, 12, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 37, 37, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/726 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493247433 none CC(C)S(=O)(=O)CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 40, 48, 48, 13, 9, 13, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 40, 40, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247433 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433 Building ZINC001493247433 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247433 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 725) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493247433 none CC(C)S(=O)(=O)CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 37, 49, 49, 12, 8, 12, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 37, 37, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 726) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493247433 none CC(C)S(=O)(=O)CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 40, 48, 48, 13, 9, 13, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 40, 40, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247433 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247433 Building ZINC001493247450 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247450 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/727 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493247450 none CC(C)S(=O)(=O)CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 36, 46, 46, 12, 9, 12, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 36, 36, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/728 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493247450 none CC(C)S(=O)(=O)CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 37, 47, 47, 10, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 37, 37, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247450 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450 Building ZINC001493247450 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247450 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 727) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493247450 none CC(C)S(=O)(=O)CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 36, 46, 46, 12, 9, 12, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 36, 36, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 728) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493247450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493247450 none CC(C)S(=O)(=O)CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 37, 47, 47, 10, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 37, 37, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247450 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247450 Building ZINC001493247897 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247897 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/729 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001493247897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001493247897 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 21, 21, 47, 47, 47, 47, 50, 50, 47, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 47, 50, 50, 47, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/730 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/730' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001493247897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001493247897 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 23, 23, 48, 48, 48, 48, 50, 50, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 48, 50, 50, 48, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247897 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897 Building ZINC001493247897 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247897 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 729) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001493247897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001493247897 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 21, 21, 47, 47, 47, 47, 50, 50, 47, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 47, 50, 50, 47, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 730) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001493247897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001493247897 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 23, 23, 48, 48, 48, 48, 50, 50, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 48, 50, 50, 48, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247897 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247897 Building ZINC001493247911 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247911 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/731 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001493247911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001493247911 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 21, 21, 47, 47, 47, 47, 50, 50, 47, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 47, 50, 50, 47, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/732 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001493247911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001493247911 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 21, 21, 48, 48, 48, 48, 50, 50, 48, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 48, 50, 50, 48, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247911 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911 Building ZINC001493247911 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247911 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 731) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001493247911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001493247911 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 21, 21, 47, 47, 47, 47, 50, 50, 47, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 47, 50, 50, 47, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 732) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001493247911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001493247911 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 21, 21, 48, 48, 48, 48, 50, 50, 48, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 48, 50, 50, 48, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247911 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247911 Building ZINC001493247916 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247916 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/733 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001493247916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493247916 none CC(C)(C)n1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 23, 14, 23, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/734 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/734' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001493247916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493247916 none CC(C)(C)n1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 13, 24, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247916 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916 Building ZINC001493247916 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493247916 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 733) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001493247916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493247916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493247916 none CC(C)(C)n1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 23, 14, 23, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 734) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001493247916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493247916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493247916 none CC(C)(C)n1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 13, 24, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493247916 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493247916 Building ZINC001493248199 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248199 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/735 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001493248199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001493248199 none Cc1noc(CCC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 21, 9, 7, 9, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 24, 24, 21, 21, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/736 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/736' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001493248199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001493248199 none Cc1noc(CCC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 22, 20, 11, 9, 11, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 22, 22, 20, 20, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248199 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199 Building ZINC001493248199 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248199 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 735) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001493248199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001493248199 none Cc1noc(CCC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 21, 9, 7, 9, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 24, 24, 21, 21, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 736) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001493248199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001493248199 none Cc1noc(CCC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 22, 20, 11, 9, 11, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 22, 22, 20, 20, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248199 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248199 Building ZINC001493248206 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248206 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/737 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001493248206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001493248206 none Cc1noc(CCC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 22, 9, 8, 9, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 24, 24, 22, 22, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/738 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/738' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001493248206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001493248206 none Cc1noc(CCC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 24, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 26, 26, 24, 24, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248206 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206 Building ZINC001493248206 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248206 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 737) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001493248206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001493248206 none Cc1noc(CCC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 22, 9, 8, 9, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 24, 24, 22, 22, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 738) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001493248206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001493248206 none Cc1noc(CCC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 24, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 26, 26, 24, 24, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248206 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248206 Building ZINC001493248217 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248217 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/739 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1) `ZINC001493248217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248217 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 20, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/740 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/740' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1) `ZINC001493248217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248217 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 23, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248217 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217 Building ZINC001493248217 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248217 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 739) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1) `ZINC001493248217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248217 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 20, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 740) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1) `ZINC001493248217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248217 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 23, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248217 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248217 Building ZINC001493248218 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248218 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/741 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1) `ZINC001493248218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248218 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 21, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/742 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/742' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1) `ZINC001493248218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248218 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 19, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248218 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218 Building ZINC001493248218 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248218 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 741) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1) `ZINC001493248218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248218 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 21, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 742) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1) `ZINC001493248218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248218 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 19, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248218 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248218 Building ZINC001493248220 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248220 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/743 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1) `ZINC001493248220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248220 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 16, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/744 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1) `ZINC001493248220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248220 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 19, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248220 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220 Building ZINC001493248220 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248220 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 743) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1) `ZINC001493248220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248220 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 16, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 744) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1) `ZINC001493248220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248220 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 19, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248220 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248220 Building ZINC001493248224 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248224 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/745 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1) `ZINC001493248224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248224 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 21, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/746 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1) `ZINC001493248224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248224 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 19, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248224 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224 Building ZINC001493248224 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248224 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 745) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1) `ZINC001493248224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248224 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 21, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 746) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1) `ZINC001493248224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248224 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCn3ccnc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 19, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248224 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248224 Building ZINC001493248479 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248479 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/747 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493248479 none Cc1nn(C)cc1CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 33, 13, 7, 13, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 33, 33, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/748 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/748' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493248479 none Cc1nn(C)cc1CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 10, 6, 10, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 32, 32, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248479 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479 Building ZINC001493248479 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248479 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 747) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)cc1CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493248479 none Cc1nn(C)cc1CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 33, 13, 7, 13, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 33, 33, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 748) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)cc1CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493248479 none Cc1nn(C)cc1CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 10, 6, 10, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 32, 32, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248479 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248479 Building ZINC001493248481 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248481 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/749 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nncn3c2)C1) `ZINC001493248481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493248481 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nncn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 20, 20, 20, 20, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/750 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nncn3c2)C1) `ZINC001493248481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493248481 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nncn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 17, 19, 19, 19, 19, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248481 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481 Building ZINC001493248481 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248481 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 749) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nncn3c2)C1) `ZINC001493248481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493248481 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nncn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 20, 20, 20, 20, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 750) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nncn3c2)C1) `ZINC001493248481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493248481 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nncn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 17, 19, 19, 19, 19, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248481 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248481 Building ZINC001493248489 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248489 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/751 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248489 none COCCOCCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 17, 17, 10, 9, 10, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/752 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248489 none COCCOCCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 31, 19, 19, 10, 8, 10, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248489 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489 Building ZINC001493248489 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248489 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 751) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248489 none COCCOCCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 17, 17, 10, 9, 10, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 752) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493248489 none COCCOCCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 31, 19, 19, 10, 8, 10, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248489 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248489 Building ZINC001493248977 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248977 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/753 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493248977 none Cn1nccc1CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 29, 14, 10, 14, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 29, 29, 29, 29, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/754 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493248977 none Cn1nccc1CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 34, 16, 13, 16, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 34, 34, 34, 34, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248977 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977 Building ZINC001493248977 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248977 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 753) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493248977 none Cn1nccc1CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 29, 14, 10, 14, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 29, 29, 29, 29, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 754) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493248977 none Cn1nccc1CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 34, 16, 13, 16, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 34, 34, 34, 34, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248977 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248977 Building ZINC001493248978 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248978 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/755 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493248978 none Cn1nccc1CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 29, 13, 10, 13, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 29, 29, 29, 29, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/756 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/756' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493248978 none Cn1nccc1CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 28, 28, 13, 11, 13, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 28, 28, 28, 28, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248978 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978 Building ZINC001493248978 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493248978 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 755) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493248978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493248978 none Cn1nccc1CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 29, 13, 10, 13, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 29, 29, 29, 29, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 756) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493248978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493248978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493248978 none Cn1nccc1CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 28, 28, 13, 11, 13, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 28, 28, 28, 28, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493248978 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493248978 Building ZINC001493249130 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493249130 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/757 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)COc2cccnc2)C1) `ZINC001493249130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493249130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493249130 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)COc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 8, 8, 23, 41, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 23, 23, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/758 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/758' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)COc2cccnc2)C1) `ZINC001493249130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493249130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493249130 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)COc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 10, 10, 21, 38, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 21, 21, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493249130 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130 Building ZINC001493249130 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493249130 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 757) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)COc2cccnc2)C1) `ZINC001493249130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493249130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493249130 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)COc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 8, 8, 23, 41, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 23, 23, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 758) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)COc2cccnc2)C1) `ZINC001493249130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493249130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493249130 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)COc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 10, 10, 21, 38, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 21, 21, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493249130 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249130 Building ZINC001493249133 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493249133 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/759 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COc2cccnc2)C1) `ZINC001493249133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493249133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493249133 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 24, 41, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 24, 24, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/760 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COc2cccnc2)C1) `ZINC001493249133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493249133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493249133 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 24, 38, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 24, 24, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493249133 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133 Building ZINC001493249133 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493249133 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 759) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COc2cccnc2)C1) `ZINC001493249133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493249133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493249133 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 24, 41, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 24, 24, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 760) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COc2cccnc2)C1) `ZINC001493249133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493249133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493249133 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 1, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 24, 38, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 24, 24, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493249133 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249133 Building ZINC001493249572 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493249572 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/761 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncncc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493249572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493249572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001493249572 none CCc1ncncc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 45, 22, 45, 45, 22, 14, 22, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 31, 45, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/762 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncncc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493249572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493249572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001493249572 none CCc1ncncc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 24, 46, 46, 24, 13, 24, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 24, 46, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493249572 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572 Building ZINC001493249572 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493249572 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 761) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncncc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493249572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493249572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001493249572 none CCc1ncncc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 45, 22, 45, 45, 22, 14, 22, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 31, 45, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 762) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ncncc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493249572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493249572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001493249572 none CCc1ncncc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 24, 46, 46, 24, 13, 24, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 24, 46, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493249572 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249572 Building ZINC001493249589 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493249589 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/763 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493249589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493249589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493249589 none CN(C)C(=O)CCCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 35, 38, 15, 12, 15, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 42, 43, 42, 42, 38, 38, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/764 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/764' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493249589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493249589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493249589 none CN(C)C(=O)CCCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 50, 35, 39, 15, 13, 15, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 40, 41, 41, 41, 39, 39, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 225 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493249589 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589 Building ZINC001493249589 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493249589 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 763) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493249589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493249589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493249589 none CN(C)C(=O)CCCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 35, 38, 15, 12, 15, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 42, 43, 42, 42, 38, 38, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 764) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493249589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493249589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493249589 none CN(C)C(=O)CCCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 50, 35, 39, 15, 13, 15, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 40, 41, 41, 41, 39, 39, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 225 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493249589 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249589 Building ZINC001493249600 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493249600 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/765 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnc(CC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)[nH]1) `ZINC001493249600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493249600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493249600 none CCc1cnc(CC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 6, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 29, 28, 7, 5, 7, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 50, 50, 50, 50, 50, 29, 28, 28, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/766 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnc(CC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)[nH]1) `ZINC001493249600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493249600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493249600 none CCc1cnc(CC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 6, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 28, 27, 8, 6, 8, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 28, 28, 50, 50, 50, 50, 50, 28, 27, 27, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493249600 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600 Building ZINC001493249600 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493249600 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 765) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnc(CC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)[nH]1) `ZINC001493249600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493249600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493249600 none CCc1cnc(CC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 6, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 29, 28, 7, 5, 7, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 50, 50, 50, 50, 50, 29, 28, 28, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 766) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnc(CC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)[nH]1) `ZINC001493249600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493249600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493249600 none CCc1cnc(CC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 6, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 28, 27, 8, 6, 8, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 28, 28, 50, 50, 50, 50, 50, 28, 27, 27, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493249600 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249600 Building ZINC001493249601 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493249601 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/767 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnc(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)[nH]1) `ZINC001493249601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493249601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493249601 none CCc1cnc(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 6, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 28, 27, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 28, 28, 50, 50, 50, 50, 50, 28, 27, 27, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/768 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/768' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnc(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)[nH]1) `ZINC001493249601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493249601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493249601 none CCc1cnc(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 6, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 26, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 30, 30, 50, 50, 50, 50, 50, 30, 26, 26, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493249601 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601 Building ZINC001493249601 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493249601 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 767) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnc(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)[nH]1) `ZINC001493249601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493249601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493249601 none CCc1cnc(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 6, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 28, 27, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 28, 28, 50, 50, 50, 50, 50, 28, 27, 27, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 768) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cnc(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)[nH]1) `ZINC001493249601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493249601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493249601 none CCc1cnc(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 6, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 26, 7, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 30, 30, 50, 50, 50, 50, 50, 30, 26, 26, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493249601 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493249601 Building ZINC001493287750 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493287750 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/769 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493287750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493287750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493287750 none CCCS(=O)(=O)CC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 36, 46, 46, 12, 12, 12, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 36, 36, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/770 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/770' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493287750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493287750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493287750 none CCCS(=O)(=O)CC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 41, 48, 48, 16, 16, 16, 7, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 41, 41, 16, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493287750 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750 Building ZINC001493287750 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493287750 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 769) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493287750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493287750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493287750 none CCCS(=O)(=O)CC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 36, 46, 46, 12, 12, 12, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 36, 36, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 770) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493287750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493287750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493287750 none CCCS(=O)(=O)CC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 41, 48, 48, 16, 16, 16, 7, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 41, 41, 16, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493287750 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287750 Building ZINC001493287752 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493287752 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/771 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493287752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493287752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493287752 none CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 37, 45, 45, 13, 13, 13, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 37, 37, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/772 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493287752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493287752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493287752 none CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 36, 47, 47, 11, 11, 11, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 36, 36, 11, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493287752 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752 Building ZINC001493287752 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493287752 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 771) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493287752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493287752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493287752 none CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 37, 45, 45, 13, 13, 13, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 37, 37, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 772) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493287752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493287752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493287752 none CCCS(=O)(=O)CC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 36, 47, 47, 11, 11, 11, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 36, 36, 11, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493287752 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493287752 Building ZINC001493315590 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493315590 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/773 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493315590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315590 none CC[C@@]1(C(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 25, 25, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/774 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/774' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493315590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315590 none CC[C@@]1(C(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 21, 21, 7, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493315590 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590 Building ZINC001493315590 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493315590 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 773) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493315590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315590 none CC[C@@]1(C(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 25, 25, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 774) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493315590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315590 none CC[C@@]1(C(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 21, 21, 7, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493315590 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315590 Building ZINC001493315592 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493315592 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/775 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)N[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493315592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315592 none CC[C@]1(C(=O)N[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 20, 20, 7, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/776 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)N[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493315592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315592 none CC[C@]1(C(=O)N[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 23, 23, 10, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 139 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493315592 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592 Building ZINC001493315592 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493315592 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 775) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)N[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493315592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315592 none CC[C@]1(C(=O)N[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 20, 20, 7, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 776) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)N[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493315592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315592 none CC[C@]1(C(=O)N[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 23, 23, 10, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 139 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493315592 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315592 Building ZINC001493315594 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493315594 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/777 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493315594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315594 none CC[C@]1(C(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 19, 19, 7, 7, 7, 7, 7, 4, 1, 6, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/778 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493315594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315594 none CC[C@]1(C(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 19, 19, 7, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 133 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493315594 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594 Building ZINC001493315594 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493315594 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 777) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493315594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315594 none CC[C@]1(C(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 19, 19, 7, 7, 7, 7, 7, 4, 1, 6, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 778) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493315594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315594 none CC[C@]1(C(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 19, 19, 7, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 133 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493315594 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315594 Building ZINC001493315596 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493315596 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/779 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)N[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493315596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315596 none CC[C@@]1(C(=O)N[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 20, 20, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 134 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/780 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)N[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493315596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315596 none CC[C@@]1(C(=O)N[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 19, 19, 8, 8, 8, 8, 8, 4, 1, 7, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493315596 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596 Building ZINC001493315596 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493315596 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 779) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)N[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493315596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315596 none CC[C@@]1(C(=O)N[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 20, 20, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 134 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 780) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)N[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O) `ZINC001493315596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493315596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001493315596 none CC[C@@]1(C(=O)N[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 19, 19, 8, 8, 8, 8, 8, 4, 1, 7, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493315596 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493315596 Building ZINC001493358272 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493358272 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/781 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/782 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 18, 18, 35, 35, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/783 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/783' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/784 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/784' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 18, 18, 35, 35, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493358272 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 Building ZINC001493358272 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493358272 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 781) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 782) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 18, 18, 35, 35, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 783) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 784) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 18, 18, 35, 35, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493358272 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 Building ZINC001493358272 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493358272 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 781) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 782) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 18, 18, 35, 35, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 783) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 784) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 18, 18, 35, 35, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493358272 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 Building ZINC001493358272 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493358272 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 781) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 782) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 18, 18, 35, 35, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 783) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 784) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358272.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493358272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358272 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 18, 18, 35, 35, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493358272 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358272 Building ZINC001493358273 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493358273 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/785 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/786 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/786' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 15, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/787 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/787' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/788 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/788' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 15, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493358273 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 Building ZINC001493358273 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493358273 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 785) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 786) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 15, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 787) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 788) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 15, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493358273 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 Building ZINC001493358273 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493358273 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 785) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 786) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 15, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 787) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 788) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 15, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493358273 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 Building ZINC001493358273 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493358273 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 785) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 786) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 15, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 787) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 788) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1) `ZINC001493358273.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493358273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493358273 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C[C@@H]1CCS(=O)(=O)C1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 15, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493358273 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493358273 Building ZINC001493384230 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493384230 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/789 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(C)(C)S(C)(=O)=O)C1) `ZINC001493384230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493384230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493384230 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(C)(C)S(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 20, 20, 20, 47, 47, 47, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 47, 47, 47, 47, 47, 47, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/790 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/790' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(C)(C)S(C)(=O)=O)C1) `ZINC001493384230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493384230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493384230 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(C)(C)S(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 19, 19, 19, 45, 45, 45, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 19, 45, 45, 45, 45, 45, 45, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493384230 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230 Building ZINC001493384230 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493384230 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 789) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CC[C@@H](NC(=O)C(C)(C)S(C)(=O)=O)C1) `ZINC001493384230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493384230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493384230 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(C)(C)S(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 20, 20, 20, 47, 47, 47, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 47, 47, 47, 47, 47, 47, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 790) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CC[C@@H](NC(=O)C(C)(C)S(C)(=O)=O)C1) `ZINC001493384230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493384230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493384230 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(C)(C)S(C)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 19, 19, 19, 45, 45, 45, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 19, 45, 45, 45, 45, 45, 45, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493384230 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493384230 Building ZINC001493418616 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493418616 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/791 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2) `ZINC001493418616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493418616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493418616 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 16, 16, 16, 16, 33, 33, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 16, 16, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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/83982/xcb-8058097.54/working/building/ZINC001493418616 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/792 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/792' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2) `ZINC001493418616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493418616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493418616 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 35, 35, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 18, 18, 50, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493418616 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616 Building ZINC001493418616 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493418616 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 791) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2) `ZINC001493418616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493418616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493418616 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 16, 16, 16, 16, 33, 33, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 16, 16, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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/83982/xcb-8058097.54/working/building/ZINC001493418616 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 792) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2) `ZINC001493418616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493418616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493418616 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 18, 18, 18, 18, 35, 35, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 18, 18, 50, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493418616 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418616 Building ZINC001493418617 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493418617 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/793 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2) `ZINC001493418617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493418617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493418617 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 20, 20, 20, 20, 20, 20, 34, 34, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 20, 20, 50, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/794 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/794' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2) `ZINC001493418617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493418617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493418617 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 16, 16, 16, 31, 31, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 16, 16, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493418617 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617 Building ZINC001493418617 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493418617 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 793) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2) `ZINC001493418617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493418617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493418617 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 20, 20, 20, 20, 20, 20, 34, 34, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 20, 20, 50, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 794) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2) `ZINC001493418617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493418617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493418617 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)c1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 16, 16, 16, 31, 31, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 16, 16, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493418617 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493418617 Building ZINC001493420324 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493420324 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/795 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2) `ZINC001493420324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493420324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493420324 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 9, 12, 12, 12, 12, 12, 19, 19, 30, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 30, 30, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 157 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/796 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/796' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2) `ZINC001493420324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493420324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493420324 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 11, 11, 11, 11, 11, 19, 19, 32, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 11, 32, 32, 50, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493420324 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324 Building ZINC001493420324 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493420324 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 795) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2) `ZINC001493420324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493420324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493420324 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 9, 12, 12, 12, 12, 12, 19, 19, 30, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 30, 30, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 157 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 796) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2) `ZINC001493420324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493420324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493420324 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 11, 11, 11, 11, 11, 19, 19, 32, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 11, 32, 32, 50, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493420324 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420324 Building ZINC001493420328 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493420328 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/797 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2) `ZINC001493420328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493420328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493420328 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 12, 12, 12, 12, 20, 20, 28, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 28, 28, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 133 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/798 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/798' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2) `ZINC001493420328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493420328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493420328 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 15, 15, 15, 21, 21, 32, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 15, 15, 32, 32, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493420328 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328 Building ZINC001493420328 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493420328 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 797) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2) `ZINC001493420328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493420328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493420328 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 12, 12, 12, 12, 20, 20, 28, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 12, 28, 28, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 133 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 798) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2) `ZINC001493420328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493420328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493420328 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC12CCN(C(=O)Cc1nc[nH]n1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 15, 15, 15, 21, 21, 32, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 15, 15, 32, 32, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493420328 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493420328 Building ZINC001493427123 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493427123 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/799 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2CCC3(C[C@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001493427123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493427123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493427123 none Cn1ncc(C(=O)N2CCC3(C[C@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 25, 46, 25, 25, 25, 25, 25, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83982/xcb-8058097.54/working/building/ZINC001493427123 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/800 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2CCC3(C[C@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001493427123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493427123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493427123 none Cn1ncc(C(=O)N2CCC3(C[C@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 25, 45, 25, 25, 25, 25, 25, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493427123 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123 Building ZINC001493427123 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493427123 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 799) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2CCC3(C[C@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001493427123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493427123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493427123 none Cn1ncc(C(=O)N2CCC3(C[C@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 25, 46, 25, 25, 25, 25, 25, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83982/xcb-8058097.54/working/building/ZINC001493427123 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 800) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2CCC3(C[C@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001493427123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493427123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493427123 none Cn1ncc(C(=O)N2CCC3(C[C@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 25, 45, 25, 25, 25, 25, 25, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493427123 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427123 Building ZINC001493427130 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493427130 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/801 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2CCC3(C[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001493427130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493427130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493427130 none Cn1ncc(C(=O)N2CCC3(C[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 23, 42, 23, 23, 23, 23, 23, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83982/xcb-8058097.54/working/building/ZINC001493427130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/802 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/802' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2CCC3(C[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001493427130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493427130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493427130 none Cn1ncc(C(=O)N2CCC3(C[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 27, 45, 27, 27, 27, 27, 27, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493427130 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130 Building ZINC001493427130 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493427130 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 801) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2CCC3(C[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001493427130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493427130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493427130 none Cn1ncc(C(=O)N2CCC3(C[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 23, 42, 23, 23, 23, 23, 23, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/83982/xcb-8058097.54/working/building/ZINC001493427130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 802) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2CCC3(C[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001493427130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493427130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493427130 none Cn1ncc(C(=O)N2CCC3(C[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 27, 45, 27, 27, 27, 27, 27, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493427130 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493427130 Building ZINC001493499224 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493499224 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/803 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNCC1(CS(C)(=O)=O)CC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001493499224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493499224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493499224 none CN(CCNCC1(CS(C)(=O)=O)CC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 7, 7, 8, 12, 43, 47, 50, 50, 50, 43, 43, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 8, 12, 12, 47, 47, 50, 50, 50, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/804 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/804' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNCC1(CS(C)(=O)=O)CC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001493499224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493499224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493499224 none CN(CCNCC1(CS(C)(=O)=O)CC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 7, 16, 39, 44, 50, 50, 50, 39, 39, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 7, 16, 16, 44, 44, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493499224 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224 Building ZINC001493499224 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493499224 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 803) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCNCC1(CS(C)(=O)=O)CC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001493499224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493499224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493499224 none CN(CCNCC1(CS(C)(=O)=O)CC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 7, 7, 8, 12, 43, 47, 50, 50, 50, 43, 43, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 8, 12, 12, 47, 47, 50, 50, 50, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 804) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/804: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCNCC1(CS(C)(=O)=O)CC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001493499224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493499224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493499224 none CN(CCNCC1(CS(C)(=O)=O)CC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 5, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 7, 16, 39, 44, 50, 50, 50, 39, 39, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 7, 16, 16, 44, 44, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493499224 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493499224 Building ZINC001493508060 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508060 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/805 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cnn[nH]1)C1CC1) `ZINC001493508060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508060 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cnn[nH]1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 16, 16, 16, 43, 46, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 16, 43, 43, 46, 46, 50, 13, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/806 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/806' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cnn[nH]1)C1CC1) `ZINC001493508060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508060 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cnn[nH]1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 10, 10, 16, 16, 16, 34, 39, 48, 48, 48, 48, 48, 10, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 16, 34, 34, 39, 39, 48, 13, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508060 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060 Building ZINC001493508060 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508060 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 805) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)CCc1cnn[nH]1)C1CC1) `ZINC001493508060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508060 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cnn[nH]1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 16, 16, 16, 43, 46, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 16, 43, 43, 46, 46, 50, 13, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 806) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)CCc1cnn[nH]1)C1CC1) `ZINC001493508060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508060 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cnn[nH]1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 10, 10, 16, 16, 16, 34, 39, 48, 48, 48, 48, 48, 10, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 16, 34, 34, 39, 39, 48, 13, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508060 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508060 Building ZINC001493508061 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508061 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/807 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cnn[nH]1)C1CC1) `ZINC001493508061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508061 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cnn[nH]1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 17, 17, 17, 37, 42, 50, 50, 50, 50, 50, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 37, 37, 42, 42, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/808 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cnn[nH]1)C1CC1) `ZINC001493508061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508061 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cnn[nH]1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 14, 14, 18, 18, 18, 42, 46, 50, 50, 50, 50, 50, 14, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 18, 42, 42, 46, 46, 50, 15, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508061 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061 Building ZINC001493508061 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508061 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 807) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)CCc1cnn[nH]1)C1CC1) `ZINC001493508061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508061 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cnn[nH]1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 17, 17, 17, 37, 42, 50, 50, 50, 50, 50, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 37, 37, 42, 42, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 808) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)CCc1cnn[nH]1)C1CC1) `ZINC001493508061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508061 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cnn[nH]1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 14, 14, 18, 18, 18, 42, 46, 50, 50, 50, 50, 50, 14, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 18, 42, 42, 46, 46, 50, 15, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508061 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508061 Building ZINC001493508108 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508108 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/809 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493508108 none CN(C)CCCC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 41, 42, 16, 16, 16, 11, 8, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 48, 50, 48, 48, 42, 42, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/810 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493508108 none CN(C)CCCC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 36, 12, 12, 12, 8, 6, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 49, 46, 46, 36, 36, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508108 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108 Building ZINC001493508108 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508108 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 809) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCCC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493508108 none CN(C)CCCC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 41, 42, 16, 16, 16, 11, 8, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 48, 50, 48, 48, 42, 42, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 810) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCCC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493508108 none CN(C)CCCC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 36, 12, 12, 12, 8, 6, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 49, 46, 46, 36, 36, 12, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508108 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508108 Building ZINC001493508109 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508109 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/811 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493508109 none CN(C)CCCC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 41, 37, 14, 14, 14, 9, 7, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 10, 10, 50, 50, 50, 50, 50, 50, 49, 47, 46, 46, 37, 37, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/812 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493508109 none CN(C)CCCC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 41, 15, 15, 15, 10, 8, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 41, 41, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508109 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109 Building ZINC001493508109 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508109 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 811) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCCC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493508109 none CN(C)CCCC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 41, 37, 14, 14, 14, 9, 7, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 10, 10, 50, 50, 50, 50, 50, 50, 49, 47, 46, 46, 37, 37, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 812) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCCC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493508109 none CN(C)CCCC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 41, 15, 15, 15, 10, 8, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 41, 41, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508109 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508109 Building ZINC001493508372 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508372 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/813 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1) `ZINC001493508372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493508372 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 5, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 34, 34, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 33, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 48, 48, 48, 38, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/814 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1) `ZINC001493508372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493508372 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 5, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 32, 32, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 30, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 47, 50, 50, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508372 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372 Building ZINC001493508372 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508372 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 813) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1) `ZINC001493508372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493508372 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 5, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 34, 34, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 33, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 48, 48, 48, 38, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 814) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1) `ZINC001493508372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493508372 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 5, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 32, 32, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 30, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 47, 50, 50, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508372 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508372 Building ZINC001493508376 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508376 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/815 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1) `ZINC001493508376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493508376 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 5, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 32, 32, 48, 48, 48, 49, 49, 49, 49, 49, 49, 49, 32, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 48, 49, 49, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 208 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/816 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1) `ZINC001493508376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493508376 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 5, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 30, 30, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 30, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 47, 50, 50, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 210 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508376 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376 Building ZINC001493508376 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508376 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 815) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1) `ZINC001493508376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493508376 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 5, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 32, 32, 48, 48, 48, 49, 49, 49, 49, 49, 49, 49, 32, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 48, 49, 49, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 208 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 816) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1) `ZINC001493508376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493508376 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1c[nH]c(=O)cn1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 8, 6, 1, 11, 1, 8, 5, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 30, 30, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 30, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 47, 50, 50, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 210 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508376 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508376 Building ZINC001493508645 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508645 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/817 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1) `ZINC001493508645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508645 none Cc1nc(CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 21, 21, 12, 9, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 13, 13, 50, 50, 50, 50, 50, 50, 36, 36, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 183 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/818 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1) `ZINC001493508645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508645 none Cc1nc(CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 24, 24, 24, 14, 9, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 50, 37, 37, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 184 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508645 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645 Building ZINC001493508645 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508645 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 817) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1) `ZINC001493508645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508645 none Cc1nc(CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 21, 21, 12, 9, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 13, 13, 50, 50, 50, 50, 50, 50, 36, 36, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 183 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 818) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1) `ZINC001493508645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508645 none Cc1nc(CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 24, 24, 24, 14, 9, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 50, 37, 37, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 184 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508645 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508645 Building ZINC001493508648 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508648 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/819 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1) `ZINC001493508648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508648 none Cc1nc(CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 20, 20, 20, 12, 8, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 13, 13, 50, 50, 50, 50, 50, 50, 34, 34, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/820 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1) `ZINC001493508648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508648 none Cc1nc(CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 23, 23, 23, 14, 9, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 50, 37, 37, 23, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508648 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648 Building ZINC001493508648 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508648 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 819) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1) `ZINC001493508648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508648 none Cc1nc(CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 20, 20, 20, 12, 8, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 13, 13, 50, 50, 50, 50, 50, 50, 34, 34, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 820) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1) `ZINC001493508648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493508648 none Cc1nc(CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 23, 23, 23, 14, 9, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 50, 37, 37, 23, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508648 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508648 Building ZINC001493508767 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508767 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/821 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508767 none CCC(=O)N[C@@H](C)C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 33, 16, 33, 33, 16, 16, 10, 6, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 38, 33, 33, 33, 16, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 239 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/822 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508767 none CCC(=O)N[C@@H](C)C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 35, 19, 35, 35, 19, 19, 13, 10, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 50, 50, 50, 50, 50, 40, 35, 35, 35, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 236 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508767 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767 Building ZINC001493508767 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508767 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 821) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508767 none CCC(=O)N[C@@H](C)C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 33, 16, 33, 33, 16, 16, 10, 6, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 38, 33, 33, 33, 16, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 239 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 822) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508767 none CCC(=O)N[C@@H](C)C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 35, 19, 35, 35, 19, 19, 13, 10, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 50, 50, 50, 50, 50, 40, 35, 35, 35, 19, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 236 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508767 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508767 Building ZINC001493508768 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508768 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/823 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508768 none CCC(=O)N[C@@H](C)C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 34, 23, 34, 34, 23, 23, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 36, 34, 34, 34, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 247 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/824 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508768 none CCC(=O)N[C@@H](C)C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 41, 34, 27, 34, 34, 27, 27, 14, 10, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 15, 15, 50, 50, 50, 50, 50, 41, 34, 34, 34, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 228 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508768 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768 Building ZINC001493508768 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508768 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 823) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508768 none CCC(=O)N[C@@H](C)C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 34, 23, 34, 34, 23, 23, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 36, 34, 34, 34, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 247 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 824) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508768 none CCC(=O)N[C@@H](C)C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 41, 34, 27, 34, 34, 27, 27, 14, 10, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 15, 15, 50, 50, 50, 50, 50, 41, 34, 34, 34, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 228 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508768 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508768 Building ZINC001493508770 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508770 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/825 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508770 none CCC(=O)N[C@H](C)C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 31, 19, 31, 31, 19, 19, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 14, 14, 50, 50, 50, 50, 50, 36, 31, 31, 31, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 251 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/826 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/826' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508770 none CCC(=O)N[C@H](C)C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 31, 16, 31, 31, 16, 16, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 35, 31, 31, 31, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 245 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508770 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770 Building ZINC001493508770 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508770 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 825) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508770 none CCC(=O)N[C@H](C)C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 31, 19, 31, 31, 19, 19, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 14, 14, 50, 50, 50, 50, 50, 36, 31, 31, 31, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 251 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 826) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508770 none CCC(=O)N[C@H](C)C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 31, 16, 31, 31, 16, 16, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 35, 31, 31, 31, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 245 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508770 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508770 Building ZINC001493508771 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508771 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/827 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508771 none CCC(=O)N[C@H](C)C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 41, 37, 24, 37, 37, 24, 24, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 14, 14, 50, 50, 50, 50, 50, 41, 37, 37, 37, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 240 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/828 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/828' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508771 none CCC(=O)N[C@H](C)C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 34, 23, 34, 34, 23, 23, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 36, 34, 34, 34, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 247 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508771 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771 Building ZINC001493508771 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493508771 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 827) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493508771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508771 none CCC(=O)N[C@H](C)C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 41, 37, 24, 37, 37, 24, 24, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 14, 14, 50, 50, 50, 50, 50, 41, 37, 37, 37, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 240 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 828) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493508771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493508771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493508771 none CCC(=O)N[C@H](C)C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 34, 23, 34, 34, 23, 23, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 36, 34, 34, 34, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 247 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493508771 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493508771 Building ZINC001493509172 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493509172 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/829 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C[C@H]1CCNC1=O)C1CC1) `ZINC001493509172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493509172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509172 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C[C@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 26, 26, 26, 47, 50, 50, 50, 50, 50, 50, 16, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 47, 47, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/830 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C[C@H]1CCNC1=O)C1CC1) `ZINC001493509172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493509172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509172 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C[C@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 30, 30, 30, 49, 50, 50, 50, 50, 50, 50, 20, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 30, 49, 49, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493509172 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172 Building ZINC001493509172 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493509172 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 829) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)C[C@H]1CCNC1=O)C1CC1) `ZINC001493509172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493509172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509172 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C[C@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 26, 26, 26, 47, 50, 50, 50, 50, 50, 50, 16, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 47, 47, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 830) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)C[C@H]1CCNC1=O)C1CC1) `ZINC001493509172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493509172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509172 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C[C@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 30, 30, 30, 49, 50, 50, 50, 50, 50, 50, 20, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 30, 49, 49, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493509172 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509172 Building ZINC001493509176 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493509176 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/831 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1) `ZINC001493509176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493509176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509176 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 27, 27, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 27, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 36, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/832 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1) `ZINC001493509176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493509176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509176 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 17, 17, 28, 28, 28, 47, 50, 50, 50, 50, 50, 50, 17, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 28, 47, 47, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493509176 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176 Building ZINC001493509176 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493509176 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 831) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1) `ZINC001493509176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493509176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509176 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 27, 27, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 27, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 36, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 832) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1) `ZINC001493509176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493509176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509176 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 17, 17, 28, 28, 28, 47, 50, 50, 50, 50, 50, 50, 17, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 28, 47, 47, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493509176 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509176 Building ZINC001493509177 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493509177 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/833 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1) `ZINC001493509177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493509177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509177 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 29, 29, 29, 48, 50, 50, 50, 50, 50, 50, 17, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 29, 46, 46, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/834 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/834' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1) `ZINC001493509177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493509177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509177 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 22, 22, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 22, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 28, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493509177 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177 Building ZINC001493509177 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493509177 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 833) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1) `ZINC001493509177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493509177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509177 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 29, 29, 29, 48, 50, 50, 50, 50, 50, 50, 17, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 29, 46, 46, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 834) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1) `ZINC001493509177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493509177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509177 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C[C@@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 22, 22, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 22, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 28, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493509177 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509177 Building ZINC001493509179 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493509179 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/835 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@H]1CCNC1=O)C1CC1) `ZINC001493509179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493509179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509179 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 25, 25, 31, 31, 31, 49, 50, 50, 50, 50, 50, 50, 25, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 31, 48, 48, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/836 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/836' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@H]1CCNC1=O)C1CC1) `ZINC001493509179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493509179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509179 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 19, 19, 30, 30, 30, 49, 50, 50, 50, 50, 50, 50, 19, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 30, 48, 48, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493509179 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179 Building ZINC001493509179 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493509179 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 835) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/835: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)C[C@H]1CCNC1=O)C1CC1) `ZINC001493509179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493509179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509179 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 25, 25, 31, 31, 31, 49, 50, 50, 50, 50, 50, 50, 25, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 31, 48, 48, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 836) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)C[C@H]1CCNC1=O)C1CC1) `ZINC001493509179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493509179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493509179 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@H]1CCNC1=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 19, 19, 30, 30, 30, 49, 50, 50, 50, 50, 50, 50, 19, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 30, 48, 48, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493509179 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493509179 Building ZINC001493510133 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510133 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/837 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510133 none CN1CC[C@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 50, 32, 32, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/838 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510133 none CN1CC[C@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 36, 36, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510133 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133 Building ZINC001493510133 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510133 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 837) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510133 none CN1CC[C@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 50, 32, 32, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 838) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510133 none CN1CC[C@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 36, 36, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510133 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510133 Building ZINC001493510144 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510144 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/839 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510144 none CN1CC[C@@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 36, 36, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/840 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/840' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510144 none CN1CC[C@@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 39, 50, 32, 32, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510144 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144 Building ZINC001493510144 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510144 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 839) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510144 none CN1CC[C@@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 36, 36, 27, 12, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 840) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510144 none CN1CC[C@@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 39, 50, 32, 32, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510144 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510144 Building ZINC001493510146 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510146 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/841 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510146 none CN1CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 40, 48, 35, 35, 23, 11, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48, 48, 35, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/842 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/842' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510146 none CN1CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 50, 29, 29, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510146 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146 Building ZINC001493510146 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510146 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 841) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510146 none CN1CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 40, 48, 35, 35, 23, 11, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 29, 29, 48, 48, 48, 48, 48, 48, 48, 48, 48, 35, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 842) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510146 none CN1CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 50, 29, 29, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510146 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510146 Building ZINC001493510148 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510148 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/843 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510148 none CN1CC[C@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 32, 32, 23, 11, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/844 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510148 none CN1CC[C@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 40, 49, 32, 32, 18, 12, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 25, 25, 49, 49, 49, 49, 49, 49, 49, 49, 49, 32, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510148 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148 Building ZINC001493510148 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510148 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 843) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510148 none CN1CC[C@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 32, 32, 23, 11, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 844) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O) `ZINC001493510148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510148 none CN1CC[C@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 40, 49, 32, 32, 18, 12, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 25, 25, 49, 49, 49, 49, 49, 49, 49, 49, 49, 32, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510148 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510148 Building ZINC001493510164 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510164 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/845 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1) `ZINC001493510164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493510164 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 17, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 25, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/846 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/846' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1) `ZINC001493510164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493510164 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 26, 26, 30, 30, 40, 50, 50, 50, 50, 50, 50, 50, 26, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510164 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164 Building ZINC001493510164 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510164 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 845) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1) `ZINC001493510164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493510164 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 25, 25, 34, 50, 50, 50, 50, 50, 50, 50, 17, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 25, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 846) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1) `ZINC001493510164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493510164 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 26, 26, 30, 30, 40, 50, 50, 50, 50, 50, 50, 50, 26, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510164 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510164 Building ZINC001493510166 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510166 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/847 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1) `ZINC001493510166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493510166 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 23, 23, 30, 30, 42, 50, 50, 50, 50, 50, 50, 50, 23, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 30, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/848 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1) `ZINC001493510166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493510166 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 26, 26, 38, 50, 50, 50, 50, 50, 50, 50, 16, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510166 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166 Building ZINC001493510166 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510166 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 847) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1) `ZINC001493510166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493510166 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 23, 23, 30, 30, 42, 50, 50, 50, 50, 50, 50, 50, 23, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 30, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 848) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1) `ZINC001493510166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493510166 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CCCC(=O)N1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 26, 26, 38, 50, 50, 50, 50, 50, 50, 50, 16, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510166 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510166 Building ZINC001493510492 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510492 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/849 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C) `ZINC001493510492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001493510492 none Cc1c(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 46, 46, 23, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 46, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/850 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C) `ZINC001493510492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001493510492 none Cc1c(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 44, 44, 22, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 6, 6, 50, 50, 50, 50, 50, 50, 50, 44, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510492 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492 Building ZINC001493510492 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510492 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 849) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C) `ZINC001493510492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001493510492 none Cc1c(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 46, 46, 23, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 46, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 850) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C) `ZINC001493510492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001493510492 none Cc1c(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 44, 44, 22, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 6, 6, 50, 50, 50, 50, 50, 50, 50, 44, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510492 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510492 Building ZINC001493510504 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510504 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/851 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C) `ZINC001493510504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001493510504 none Cc1c(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 47, 47, 23, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 8, 8, 50, 50, 50, 50, 50, 50, 50, 47, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/852 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C) `ZINC001493510504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001493510504 none Cc1c(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 45, 25, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 49, 49, 49, 49, 49, 49, 49, 45, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 49, 49, 49] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510504 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504 Building ZINC001493510504 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510504 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 851) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C) `ZINC001493510504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001493510504 none Cc1c(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 47, 47, 23, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 8, 8, 50, 50, 50, 50, 50, 50, 50, 47, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 852) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C) `ZINC001493510504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001493510504 none Cc1c(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 45, 25, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 49, 49, 49, 49, 49, 49, 49, 45, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 49, 49, 49] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510504 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510504 Building ZINC001493510503 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493510503 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/853 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 39, 48, 18, 18, 18, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 39, 39, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/854 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 39, 48, 18, 18, 18, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 39, 39, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/855 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/855' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 45, 49, 28, 28, 28, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 45, 45, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/856 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/856' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 45, 49, 28, 28, 28, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 45, 45, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510503 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 Building ZINC001493510503 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493510503 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 853) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 39, 48, 18, 18, 18, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 39, 39, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 854) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 39, 48, 18, 18, 18, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 39, 39, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 855) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 45, 49, 28, 28, 28, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 45, 45, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 856) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 45, 49, 28, 28, 28, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 45, 45, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510503 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 Building ZINC001493510503 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493510503 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 853) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 39, 48, 18, 18, 18, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 39, 39, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 854) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 39, 48, 18, 18, 18, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 39, 39, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 855) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 45, 49, 28, 28, 28, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 45, 45, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 856) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 45, 49, 28, 28, 28, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 45, 45, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510503 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 Building ZINC001493510503 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493510503 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 853) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 39, 48, 18, 18, 18, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 39, 39, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 854) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 39, 48, 18, 18, 18, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 39, 39, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 855) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 45, 49, 28, 28, 28, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 45, 45, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 856) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510503.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493510503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510503 none CC(C)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 45, 49, 28, 28, 28, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 45, 45, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510503 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510503 Building ZINC001493510505 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493510505 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/857 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 43, 47, 27, 27, 27, 14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 43, 43, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/858 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 43, 47, 27, 27, 27, 14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 43, 43, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/859 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/859' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 47, 49, 28, 28, 28, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 47, 47, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/860 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/860' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 47, 49, 28, 28, 28, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 47, 47, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510505 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 Building ZINC001493510505 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493510505 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 857) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 43, 47, 27, 27, 27, 14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 43, 43, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 858) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 43, 47, 27, 27, 27, 14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 43, 43, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 859) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 47, 49, 28, 28, 28, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 47, 47, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 860) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 47, 49, 28, 28, 28, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 47, 47, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510505 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 Building ZINC001493510505 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493510505 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 857) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 43, 47, 27, 27, 27, 14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 43, 43, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 858) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 43, 47, 27, 27, 27, 14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 43, 43, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 859) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 47, 49, 28, 28, 28, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 47, 47, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 860) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 47, 49, 28, 28, 28, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 47, 47, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510505 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 Building ZINC001493510505 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493510505 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 857) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 43, 47, 27, 27, 27, 14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 43, 43, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 858) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 43, 47, 27, 27, 27, 14, 8, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 19, 19, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 43, 43, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 859) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 47, 49, 28, 28, 28, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 47, 47, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 860) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493510505.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493510505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493510505 none CC(C)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 47, 49, 28, 28, 28, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 47, 47, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] 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, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510505 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510505 Building ZINC001493510781 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510781 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/861 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)COCC(F)F)C1CC1) `ZINC001493510781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493510781 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)COCC(F)F)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 17, 17, 17, 45, 50, 50, 50, 50, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 17, 45, 45, 50, 50, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/862 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)COCC(F)F)C1CC1) `ZINC001493510781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493510781 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)COCC(F)F)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 13, 13, 15, 15, 15, 47, 50, 50, 50, 50, 13, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 15, 47, 47, 50, 50, 50, 15, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510781 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781 Building ZINC001493510781 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510781 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 861) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)COCC(F)F)C1CC1) `ZINC001493510781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493510781 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)COCC(F)F)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 17, 17, 17, 45, 50, 50, 50, 50, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 17, 45, 45, 50, 50, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 862) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)COCC(F)F)C1CC1) `ZINC001493510781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493510781 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)COCC(F)F)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 13, 13, 15, 15, 15, 47, 50, 50, 50, 50, 13, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 15, 47, 47, 50, 50, 50, 15, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510781 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510781 Building ZINC001493510782 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510782 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/863 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)COCC(F)F)C1CC1) `ZINC001493510782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493510782 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)COCC(F)F)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 18, 18, 18, 48, 50, 50, 50, 50, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 18, 48, 48, 50, 50, 50, 15, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/864 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/864' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)COCC(F)F)C1CC1) `ZINC001493510782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493510782 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)COCC(F)F)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 18, 18, 18, 40, 50, 50, 50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 18, 40, 40, 50, 50, 50, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510782 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782 Building ZINC001493510782 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493510782 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 863) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)COCC(F)F)C1CC1) `ZINC001493510782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493510782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493510782 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)COCC(F)F)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 18, 18, 18, 48, 50, 50, 50, 50, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 18, 48, 48, 50, 50, 50, 15, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 864) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)COCC(F)F)C1CC1) `ZINC001493510782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493510782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493510782 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)COCC(F)F)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 12, 12, 18, 18, 18, 40, 50, 50, 50, 50, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 18, 40, 40, 50, 50, 50, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493510782 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493510782 Building ZINC001493511057 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493511057 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/865 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1) `ZINC001493511057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493511057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493511057 none Cc1cnn(CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 15, 15, 15, 7, 5, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 40, 40, 15, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/866 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1) `ZINC001493511057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493511057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493511057 none Cc1cnn(CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 17, 17, 17, 12, 7, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 46, 46, 17, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493511057 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057 Building ZINC001493511057 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493511057 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 865) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1) `ZINC001493511057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493511057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493511057 none Cc1cnn(CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 15, 15, 15, 7, 5, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 40, 40, 15, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 866) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1) `ZINC001493511057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493511057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493511057 none Cc1cnn(CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 17, 17, 17, 12, 7, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 46, 46, 17, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493511057 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511057 Building ZINC001493511058 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493511058 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/867 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1) `ZINC001493511058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493511058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493511058 none Cc1cnn(CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 15, 15, 15, 10, 6, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 12, 12, 50, 50, 50, 50, 50, 43, 43, 15, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/868 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1) `ZINC001493511058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493511058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493511058 none Cc1cnn(CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 20, 20, 20, 9, 6, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 11, 11, 50, 50, 50, 50, 50, 43, 43, 20, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493511058 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058 Building ZINC001493511058 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493511058 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 867) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1) `ZINC001493511058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493511058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493511058 none Cc1cnn(CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 15, 15, 15, 10, 6, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 12, 12, 50, 50, 50, 50, 50, 43, 43, 15, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 868) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1) `ZINC001493511058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493511058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493511058 none Cc1cnn(CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 20, 20, 20, 9, 6, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 11, 11, 50, 50, 50, 50, 50, 43, 43, 20, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493511058 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493511058 Building ZINC001493512087 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493512087 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/869 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@@H]1COC(=O)C1)C1CC1) `ZINC001493512087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493512087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493512087 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@@H]1COC(=O)C1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 17, 17, 17, 49, 50, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 17, 43, 43, 50, 50, 50, 50, 13, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/870 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/870' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@@H]1COC(=O)C1)C1CC1) `ZINC001493512087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493512087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493512087 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@@H]1COC(=O)C1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 13, 13, 13, 41, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 13, 32, 32, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493512087 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087 Building ZINC001493512087 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493512087 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 869) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)C[C@@H]1COC(=O)C1)C1CC1) `ZINC001493512087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493512087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493512087 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@@H]1COC(=O)C1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 17, 17, 17, 49, 50, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 17, 43, 43, 50, 50, 50, 50, 13, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 870) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)C[C@@H]1COC(=O)C1)C1CC1) `ZINC001493512087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493512087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493512087 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C[C@@H]1COC(=O)C1)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 13, 13, 13, 41, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 13, 32, 32, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493512087 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493512087 Building ZINC001493513035 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493513035 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/871 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493513035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493513035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493513035 none Cn1cncc1CCC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 45, 28, 28, 28, 14, 10, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 45, 45, 45, 45, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/872 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493513035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493513035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493513035 none Cn1cncc1CCC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 22, 22, 22, 14, 10, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 20, 20, 50, 50, 50, 50, 50, 49, 49, 49, 49, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 238 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493513035 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035 Building ZINC001493513035 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493513035 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 871) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493513035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493513035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493513035 none Cn1cncc1CCC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 45, 28, 28, 28, 14, 10, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 50, 45, 45, 45, 45, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 872) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493513035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493513035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493513035 none Cn1cncc1CCC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 22, 22, 22, 14, 10, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 20, 20, 50, 50, 50, 50, 50, 49, 49, 49, 49, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 238 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493513035 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513035 Building ZINC001493513036 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493513036 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/873 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493513036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493513036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493513036 none Cn1cncc1CCC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 26, 26, 26, 20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 50, 50, 50, 50, 50, 49, 49, 49, 49, 26, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/874 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/874' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493513036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493513036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493513036 none Cn1cncc1CCC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 42, 25, 25, 25, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 42, 42, 42, 42, 25, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493513036 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036 Building ZINC001493513036 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493513036 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 873) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493513036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493513036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493513036 none Cn1cncc1CCC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 26, 26, 26, 20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 50, 50, 50, 50, 50, 49, 49, 49, 49, 26, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 874) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493513036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493513036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493513036 none Cn1cncc1CCC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 42, 25, 25, 25, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 42, 42, 42, 42, 25, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493513036 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493513036 Building ZINC001493514278 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493514278 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/875 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493514278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493514278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493514278 none Cc1nn(C)cc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 49, 28, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 12, 12, 50, 50, 50, 50, 50, 50, 50, 49, 28, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/876 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/876' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493514278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493514278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493514278 none Cc1nn(C)cc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 48, 48, 27, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493514278 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278 Building ZINC001493514278 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493514278 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 875) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)cc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493514278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493514278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493514278 none Cc1nn(C)cc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 49, 28, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 12, 12, 50, 50, 50, 50, 50, 50, 50, 49, 28, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 876) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)cc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493514278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493514278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493514278 none Cc1nn(C)cc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 48, 48, 27, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493514278 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514278 Building ZINC001493514280 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493514280 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/877 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493514280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493514280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493514280 none Cc1nn(C)cc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 48, 48, 29, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 12, 12, 50, 50, 50, 50, 50, 50, 50, 48, 29, 29, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/878 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493514280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493514280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493514280 none Cc1nn(C)cc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 48, 48, 28, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 14, 14, 50, 50, 50, 50, 50, 50, 50, 48, 28, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493514280 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280 Building ZINC001493514280 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493514280 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 877) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)cc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493514280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493514280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493514280 none Cc1nn(C)cc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 48, 48, 29, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 12, 12, 50, 50, 50, 50, 50, 50, 50, 48, 29, 29, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 878) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)cc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493514280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493514280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493514280 none Cc1nn(C)cc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 48, 48, 28, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 14, 14, 50, 50, 50, 50, 50, 50, 50, 48, 28, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493514280 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514280 Building ZINC001493514903 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493514903 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/879 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCCC(N)=O)C1CC1) `ZINC001493514903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493514903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493514903 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCCC(N)=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 23, 23, 29, 29, 29, 42, 42, 50, 50, 50, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 29, 42, 42, 46, 46, 48, 48, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/880 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCCC(N)=O)C1CC1) `ZINC001493514903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493514903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493514903 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCCC(N)=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 16, 16, 24, 24, 24, 36, 35, 50, 50, 50, 16, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 24, 36, 36, 41, 41, 48, 46, 50, 50, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493514903 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903 Building ZINC001493514903 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493514903 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 879) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)CCCC(N)=O)C1CC1) `ZINC001493514903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493514903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493514903 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCCC(N)=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 23, 23, 29, 29, 29, 42, 42, 50, 50, 50, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 29, 42, 42, 46, 46, 48, 48, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 880) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)CCCC(N)=O)C1CC1) `ZINC001493514903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493514903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493514903 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCCC(N)=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 16, 16, 24, 24, 24, 36, 35, 50, 50, 50, 16, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 24, 36, 36, 41, 41, 48, 46, 50, 50, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493514903 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514903 Building ZINC001493514905 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493514905 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/881 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCCC(N)=O)C1CC1) `ZINC001493514905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493514905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493514905 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCCC(N)=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 18, 18, 21, 21, 21, 38, 36, 50, 50, 50, 18, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 38, 38, 43, 43, 48, 47, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/882 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCCC(N)=O)C1CC1) `ZINC001493514905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493514905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493514905 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCCC(N)=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 27, 27, 27, 41, 41, 50, 50, 50, 22, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 27, 41, 41, 46, 46, 47, 48, 50, 50, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 263 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493514905 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905 Building ZINC001493514905 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493514905 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 881) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)CCCC(N)=O)C1CC1) `ZINC001493514905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493514905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493514905 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCCC(N)=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 18, 18, 21, 21, 21, 38, 36, 50, 50, 50, 18, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 38, 38, 43, 43, 48, 47, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 882) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/882: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)CCCC(N)=O)C1CC1) `ZINC001493514905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493514905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493514905 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCCC(N)=O)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 27, 27, 27, 41, 41, 50, 50, 50, 22, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 27, 41, 41, 46, 46, 47, 48, 50, 50, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 263 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493514905 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493514905 Building ZINC001493515422 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515422 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/883 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493515422 none CCNC(=O)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 28, 34, 15, 15, 15, 10, 6, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 34, 28, 28, 15, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/884 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493515422 none CCNC(=O)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 30, 34, 17, 17, 17, 12, 9, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 34, 30, 30, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515422 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422 Building ZINC001493515422 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515422 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 883) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493515422 none CCNC(=O)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 28, 34, 15, 15, 15, 10, 6, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 34, 28, 28, 15, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 884) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493515422 none CCNC(=O)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 30, 34, 17, 17, 17, 12, 9, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 34, 30, 30, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515422 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515422 Building ZINC001493515424 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515424 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/885 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493515424 none CCNC(=O)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 28, 34, 19, 19, 19, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 16, 16, 50, 50, 50, 50, 50, 34, 28, 28, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 253 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/886 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493515424 none CCNC(=O)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 28, 32, 15, 15, 15, 10, 6, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 32, 28, 28, 15, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515424 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424 Building ZINC001493515424 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515424 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 885) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493515424 none CCNC(=O)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 28, 34, 19, 19, 19, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 16, 16, 50, 50, 50, 50, 50, 34, 28, 28, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 253 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 886) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/886: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493515424 none CCNC(=O)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 28, 32, 15, 15, 15, 10, 6, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 32, 28, 28, 15, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515424 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515424 Building ZINC001493515539 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515539 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/887 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1) `ZINC001493515539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515539 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 26, 26, 39, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 26, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 39, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 212 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/888 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/888' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1) `ZINC001493515539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515539 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 33, 33, 41, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 33, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 42, 42, 42, 42, 42] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 220 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515539 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539 Building ZINC001493515539 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515539 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 887) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/887: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1) `ZINC001493515539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515539 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 26, 26, 39, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 26, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 39, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 212 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 888) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1) `ZINC001493515539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515539 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 33, 33, 41, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 33, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 42, 42, 42, 42, 42] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 220 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515539 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515539 Building ZINC001493515542 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515542 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/889 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1) `ZINC001493515542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515542 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 23, 23, 39, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 23, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 39, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/890 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1) `ZINC001493515542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515542 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 27, 27, 45, 45, 45, 49, 49, 49, 49, 49, 49, 49, 49, 27, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 45, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515542 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542 Building ZINC001493515542 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515542 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 889) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1) `ZINC001493515542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515542 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 23, 23, 39, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 23, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 39, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 890) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1) `ZINC001493515542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515542 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 27, 27, 45, 45, 45, 49, 49, 49, 49, 49, 49, 49, 49, 27, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 45, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515542 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515542 Building ZINC001493515545 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515545 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/891 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1) `ZINC001493515545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515545 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 29, 29, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 29, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/892 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1) `ZINC001493515545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515545 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 39, 39, 39, 47, 47, 47, 47, 47, 47, 47, 47, 24, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 39, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33, 33, 33, 33] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515545 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545 Building ZINC001493515545 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515545 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 891) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1) `ZINC001493515545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515545 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 29, 29, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 29, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 892) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1) `ZINC001493515545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515545 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 39, 39, 39, 47, 47, 47, 47, 47, 47, 47, 47, 24, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 39, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33, 33, 33, 33] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515545 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515545 Building ZINC001493515549 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515549 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/893 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1) `ZINC001493515549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515549 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 30, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 223 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/894 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1) `ZINC001493515549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515549 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 24, 24, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 24, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 232 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515549 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549 Building ZINC001493515549 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515549 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 893) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1) `ZINC001493515549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515549 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 30, 30, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 30, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 223 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 894) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)NC[C@@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1) `ZINC001493515549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001493515549 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CN2CCC1CC2)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 24, 24, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 24, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 232 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515549 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515549 Building ZINC001493515576 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515576 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/895 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493515576 none Cn1cncc1CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 19, 19, 19, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 46, 46, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/896 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493515576 none Cn1cncc1CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 43, 24, 24, 24, 16, 11, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 19, 19, 50, 50, 50, 50, 50, 43, 43, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515576 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576 Building ZINC001493515576 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515576 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 895) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493515576 none Cn1cncc1CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 19, 19, 19, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 46, 46, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 896) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493515576 none Cn1cncc1CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 43, 24, 24, 24, 16, 11, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 19, 19, 50, 50, 50, 50, 50, 43, 43, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515576 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515576 Building ZINC001493515587 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515587 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/897 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493515587 none Cn1cncc1CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 27, 27, 27, 15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 20, 20, 50, 50, 50, 50, 50, 44, 44, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/898 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493515587 none Cn1cncc1CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 21, 21, 21, 16, 11, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 18, 18, 50, 50, 50, 50, 50, 47, 47, 21, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515587 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587 Building ZINC001493515587 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493515587 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 897) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493515587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493515587 none Cn1cncc1CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 27, 27, 27, 15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 20, 20, 50, 50, 50, 50, 50, 44, 44, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 898) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493515587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493515587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493515587 none Cn1cncc1CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 21, 21, 21, 16, 11, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 18, 18, 50, 50, 50, 50, 50, 47, 47, 21, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493515587 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493515587 Building ZINC001493516115 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493516115 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/899 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493516115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493516115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493516115 none C[C@@H]1OCCO[C@@H]1C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 41, 49, 34, 34, 23, 12, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 27, 27, 49, 49, 49, 49, 49, 49, 49, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27] 50 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, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/900 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493516115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493516115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493516115 none C[C@@H]1OCCO[C@@H]1C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 38, 48, 28, 28, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 23, 48, 48, 48, 48, 48, 48, 48, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23] 50 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, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493516115 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115 Building ZINC001493516115 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493516115 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 899) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1OCCO[C@@H]1C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493516115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493516115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493516115 none C[C@@H]1OCCO[C@@H]1C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 41, 49, 34, 34, 23, 12, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 27, 27, 49, 49, 49, 49, 49, 49, 49, 34, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27] 50 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, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 900) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1OCCO[C@@H]1C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493516115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493516115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493516115 none C[C@@H]1OCCO[C@@H]1C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 38, 48, 28, 28, 17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 23, 48, 48, 48, 48, 48, 48, 48, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23] 50 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, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493516115 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516115 Building ZINC001493516122 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493516122 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/901 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493516122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493516122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493516122 none C[C@@H]1OCCO[C@@H]1C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 30, 30, 19, 9, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 20, 20, 50, 50, 50, 50, 50, 50, 50, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20] 50 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, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/902 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/902' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493516122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493516122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493516122 none C[C@@H]1OCCO[C@@H]1C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 50, 36, 36, 24, 13, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 36, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24] 50 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, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493516122 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122 Building ZINC001493516122 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493516122 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 901) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1OCCO[C@@H]1C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493516122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493516122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493516122 none C[C@@H]1OCCO[C@@H]1C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 30, 30, 19, 9, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 20, 20, 50, 50, 50, 50, 50, 50, 50, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20] 50 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, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 902) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1OCCO[C@@H]1C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493516122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493516122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493516122 none C[C@@H]1OCCO[C@@H]1C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 43, 50, 36, 36, 24, 13, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 36, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24] 50 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, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493516122 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516122 Building ZINC001493516124 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493516124 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/903 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1oc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O) `ZINC001493516124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493516124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001493516124 none Cn1oc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 36, 36, 36, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 49, 49, 49, 49, 49, 49, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 49] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/83982/xcb-8058097.54/working/building/ZINC001493516124 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/904 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/904' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1oc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O) `ZINC001493516124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493516124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001493516124 none Cn1oc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 35, 35, 35, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 33, 33, 50, 50, 50, 50, 50, 50, 35, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493516124 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124 Building ZINC001493516124 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493516124 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 903) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1oc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O) `ZINC001493516124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493516124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001493516124 none Cn1oc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 36, 36, 36, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 49, 49, 49, 49, 49, 49, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 49] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/83982/xcb-8058097.54/working/building/ZINC001493516124 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 904) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1oc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O) `ZINC001493516124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493516124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001493516124 none Cn1oc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 35, 35, 35, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 33, 33, 50, 50, 50, 50, 50, 50, 35, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493516124 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516124 Building ZINC001493516125 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493516125 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/905 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1oc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O) `ZINC001493516125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493516125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001493516125 none Cn1oc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 38, 38, 38, 26, 9, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 31, 31, 49, 49, 49, 49, 49, 49, 38, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 49] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/906 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/906' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1oc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O) `ZINC001493516125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493516125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001493516125 none Cn1oc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 37, 37, 37, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 27, 27, 50, 50, 50, 50, 50, 50, 37, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493516125 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125 Building ZINC001493516125 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493516125 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 905) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1oc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O) `ZINC001493516125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493516125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001493516125 none Cn1oc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 38, 38, 38, 26, 9, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 31, 31, 49, 49, 49, 49, 49, 49, 38, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 49] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 906) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1oc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O) `ZINC001493516125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493516125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001493516125 none Cn1oc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', '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.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 37, 37, 37, 21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 27, 27, 50, 50, 50, 50, 50, 50, 37, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493516125 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493516125 Building ZINC001493549191 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493549191 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/907 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493549191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493549191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493549191 none CCn1nncc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 33, 30, 30, 30, 16, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 33, 30, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 218 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/908 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/908' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493549191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493549191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493549191 none CCn1nncc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 29, 29, 29, 18, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 7, 7, 50, 50, 50, 50, 50, 34, 29, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493549191 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191 Building ZINC001493549191 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493549191 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 907) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493549191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493549191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493549191 none CCn1nncc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 33, 30, 30, 30, 16, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 33, 30, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 218 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 908) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493549191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493549191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493549191 none CCn1nncc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 29, 29, 29, 18, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 7, 7, 50, 50, 50, 50, 50, 34, 29, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493549191 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549191 Building ZINC001493549192 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493549192 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/909 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493549192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493549192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493549192 none CCn1nncc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 30, 30, 30, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 50, 50, 50, 50, 50, 34, 30, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/910 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/910' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493549192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493549192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493549192 none CCn1nncc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 35, 35, 31, 31, 31, 20, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 13, 50, 50, 50, 50, 50, 35, 31, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493549192 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192 Building ZINC001493549192 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493549192 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 909) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493549192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493549192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493549192 none CCn1nncc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 30, 30, 30, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 50, 50, 50, 50, 50, 34, 30, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 910) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493549192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493549192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493549192 none CCn1nncc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 35, 35, 31, 31, 31, 20, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 13, 50, 50, 50, 50, 50, 35, 31, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493549192 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493549192 Building ZINC001493553596 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493553596 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/911 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)Cn1ccccc1=O)C1CC1) `ZINC001493553596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493553596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493553596 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 16, 32, 32, 32, 46, 50, 50, 50, 50, 50, 50, 5, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 32, 46, 46, 50, 50, 50, 50, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/912 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)Cn1ccccc1=O)C1CC1) `ZINC001493553596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493553596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493553596 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 14, 29, 29, 29, 45, 50, 50, 50, 50, 50, 50, 6, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 29, 45, 45, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493553596 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596 Building ZINC001493553596 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493553596 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 911) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)Cn1ccccc1=O)C1CC1) `ZINC001493553596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493553596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493553596 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 16, 32, 32, 32, 46, 50, 50, 50, 50, 50, 50, 5, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 32, 46, 46, 50, 50, 50, 50, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 912) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)Cn1ccccc1=O)C1CC1) `ZINC001493553596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493553596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493553596 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 14, 29, 29, 29, 45, 50, 50, 50, 50, 50, 50, 6, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 29, 45, 45, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493553596 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553596 Building ZINC001493553597 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493553597 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/913 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)Cn1ccccc1=O)C1CC1) `ZINC001493553597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493553597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493553597 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 25, 25, 25, 48, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 25, 48, 48, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/914 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/914' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)Cn1ccccc1=O)C1CC1) `ZINC001493553597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493553597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493553597 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 16, 28, 28, 28, 47, 50, 50, 50, 50, 50, 50, 5, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 28, 47, 47, 50, 50, 50, 50, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493553597 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597 Building ZINC001493553597 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493553597 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 913) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)Cn1ccccc1=O)C1CC1) `ZINC001493553597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493553597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493553597 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 25, 25, 25, 48, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 25, 48, 48, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 914) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)Cn1ccccc1=O)C1CC1) `ZINC001493553597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493553597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493553597 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 16, 28, 28, 28, 47, 50, 50, 50, 50, 50, 50, 5, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 28, 47, 47, 50, 50, 50, 50, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493553597 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493553597 Building ZINC001493569049 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493569049 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/915 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001493569049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493569049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493569049 none COc1cc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 47, 47, 26, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 50, 50, 50, 50, 50, 50, 50, 47, 26, 26, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/916 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/916' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001493569049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493569049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493569049 none COc1cc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 48, 48, 25, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493569049 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049 Building ZINC001493569049 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493569049 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 915) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001493569049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493569049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493569049 none COc1cc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 47, 47, 26, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 50, 50, 50, 50, 50, 50, 50, 47, 26, 26, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 916) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001493569049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493569049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493569049 none COc1cc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 48, 48, 25, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 50, 50, 50, 50, 50, 50, 50, 48, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493569049 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569049 Building ZINC001493569051 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493569051 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/917 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001493569051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493569051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493569051 none COc1cc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 25, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 18, 18, 50, 50, 50, 50, 50, 50, 50, 49, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/918 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/918' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001493569051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493569051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493569051 none COc1cc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 25, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 12, 12, 50, 50, 50, 50, 50, 50, 50, 49, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493569051 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051 Building ZINC001493569051 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493569051 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 917) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001493569051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493569051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493569051 none COc1cc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 25, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 18, 18, 50, 50, 50, 50, 50, 50, 50, 49, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 918) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1) `ZINC001493569051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493569051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493569051 none COc1cc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 25, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 12, 12, 50, 50, 50, 50, 50, 50, 50, 49, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493569051 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493569051 Building ZINC001493576494 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493576494 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/919 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 35, 35, 18, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 35, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/920 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/920' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 35, 35, 18, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 35, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/921 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/921' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 49, 32, 32, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 10, 10, 49, 49, 49, 49, 49, 49, 49, 32, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/922 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/922' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 49, 32, 32, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 10, 10, 49, 49, 49, 49, 49, 49, 49, 32, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493576494 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 Building ZINC001493576494 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493576494 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 919) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 35, 35, 18, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 35, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 920) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 35, 35, 18, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 35, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 921) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 49, 32, 32, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 10, 10, 49, 49, 49, 49, 49, 49, 49, 32, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 922) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 49, 32, 32, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 10, 10, 49, 49, 49, 49, 49, 49, 49, 32, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493576494 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 Building ZINC001493576494 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493576494 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 919) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 35, 35, 18, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 35, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 920) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 35, 35, 18, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 35, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 921) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 49, 32, 32, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 10, 10, 49, 49, 49, 49, 49, 49, 49, 32, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 922) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 49, 32, 32, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 10, 10, 49, 49, 49, 49, 49, 49, 49, 32, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493576494 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 Building ZINC001493576494 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493576494 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 919) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 35, 35, 18, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 35, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 920) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 50, 35, 35, 18, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 35, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 921) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 49, 32, 32, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 10, 10, 49, 49, 49, 49, 49, 49, 49, 32, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 922) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576494.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493576494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576494 none C[C@@H]1[C@H](C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 49, 32, 32, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 10, 10, 49, 49, 49, 49, 49, 49, 49, 32, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493576494 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576494 Building ZINC001493576497 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493576497 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/923 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 49, 35, 35, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 49, 49, 49, 49, 49, 49, 49, 35, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/924 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/924' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 49, 35, 35, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 49, 49, 49, 49, 49, 49, 49, 35, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/925 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/925' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 30, 30, 17, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/926 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/926' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 30, 30, 17, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493576497 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 Building ZINC001493576497 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493576497 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 923) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 49, 35, 35, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 49, 49, 49, 49, 49, 49, 49, 35, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 924) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 49, 35, 35, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 49, 49, 49, 49, 49, 49, 49, 35, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 925) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 30, 30, 17, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 926) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 30, 30, 17, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493576497 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 Building ZINC001493576497 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493576497 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 923) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 49, 35, 35, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 49, 49, 49, 49, 49, 49, 49, 35, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 924) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 49, 35, 35, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 49, 49, 49, 49, 49, 49, 49, 35, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 925) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 30, 30, 17, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 926) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 30, 30, 17, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493576497 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 Building ZINC001493576497 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493576497 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 923) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 49, 35, 35, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 49, 49, 49, 49, 49, 49, 49, 35, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 924) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 49, 35, 35, 19, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 49, 49, 49, 49, 49, 49, 49, 35, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 925) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 30, 30, 17, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 926) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C) `ZINC001493576497.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493576497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493576497 none C[C@@H]1[C@H](C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 30, 30, 17, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493576497 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493576497 Building ZINC001493596465 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493596465 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/927 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cncnc1O)C1CC1) `ZINC001493596465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493596465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493596465 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cncnc1O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 19, 41, 41, 41, 50, 50, 46, 50, 50, 50, 5, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 41, 50, 50, 100, 7, 7, 7, 7, 7] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 287 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/928 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/928' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cncnc1O)C1CC1) `ZINC001493596465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493596465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493596465 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cncnc1O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 19, 38, 38, 38, 47, 47, 47, 47, 47, 47, 7, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 38, 47, 47, 94, 12, 12, 12, 12, 12] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 269 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493596465 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465 Building ZINC001493596465 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493596465 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 927) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cncnc1O)C1CC1) `ZINC001493596465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493596465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493596465 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cncnc1O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 19, 41, 41, 41, 50, 50, 46, 50, 50, 50, 5, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 41, 50, 50, 100, 7, 7, 7, 7, 7] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 287 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 928) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cncnc1O)C1CC1) `ZINC001493596465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493596465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493596465 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cncnc1O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 19, 38, 38, 38, 47, 47, 47, 47, 47, 47, 7, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 38, 47, 47, 94, 12, 12, 12, 12, 12] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 269 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493596465 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596465 Building ZINC001493596466 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493596466 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/929 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cncnc1O)C1CC1) `ZINC001493596466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493596466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493596466 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cncnc1O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 15, 33, 33, 33, 44, 44, 33, 44, 44, 44, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 33, 44, 44, 88, 13, 13, 13, 13, 13] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/930 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/930' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cncnc1O)C1CC1) `ZINC001493596466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493596466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493596466 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cncnc1O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 15, 37, 37, 37, 50, 50, 37, 50, 50, 50, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 37, 50, 50, 100, 9, 9, 9, 9, 9] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 323 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493596466 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466 Building ZINC001493596466 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493596466 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 929) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cncnc1O)C1CC1) `ZINC001493596466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493596466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493596466 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cncnc1O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 15, 33, 33, 33, 44, 44, 33, 44, 44, 44, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 33, 44, 44, 88, 13, 13, 13, 13, 13] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 930) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cncnc1O)C1CC1) `ZINC001493596466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493596466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493596466 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cncnc1O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 15, 37, 37, 37, 50, 50, 37, 50, 50, 50, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 37, 50, 50, 100, 9, 9, 9, 9, 9] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 323 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493596466 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493596466 Building ZINC001493603230 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493603230 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/931 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCC(N)=O)C1CC1) `ZINC001493603230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493603230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493603230 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 17, 30, 30, 30, 40, 40, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 30, 40, 40, 44, 44, 47, 49, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/932 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/932' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCC(N)=O)C1CC1) `ZINC001493603230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493603230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493603230 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 16, 27, 27, 27, 36, 38, 49, 49, 49, 8, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 27, 36, 36, 41, 41, 46, 49, 49, 49, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493603230 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230 Building ZINC001493603230 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493603230 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 931) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCC(N)=O)C1CC1) `ZINC001493603230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493603230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493603230 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 17, 30, 30, 30, 40, 40, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 30, 40, 40, 44, 44, 47, 49, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 932) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCC(N)=O)C1CC1) `ZINC001493603230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493603230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493603230 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 16, 27, 27, 27, 36, 38, 49, 49, 49, 8, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 27, 36, 36, 41, 41, 46, 49, 49, 49, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493603230 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603230 Building ZINC001493603232 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493603232 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/933 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCC(N)=O)C1CC1) `ZINC001493603232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493603232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493603232 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 17, 26, 26, 26, 38, 41, 50, 50, 50, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 26, 38, 38, 42, 42, 49, 50, 50, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/934 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/934' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCC(N)=O)C1CC1) `ZINC001493603232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493603232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493603232 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 27, 27, 27, 40, 41, 50, 50, 50, 7, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 27, 40, 40, 45, 45, 49, 47, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493603232 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232 Building ZINC001493603232 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493603232 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 933) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCC(N)=O)C1CC1) `ZINC001493603232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493603232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493603232 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 17, 26, 26, 26, 38, 41, 50, 50, 50, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 26, 38, 38, 42, 42, 49, 50, 50, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 934) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCC(N)=O)C1CC1) `ZINC001493603232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493603232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493603232 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 27, 27, 27, 40, 41, 50, 50, 50, 7, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 27, 40, 40, 45, 45, 49, 47, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 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, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493603232 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493603232 Building ZINC001493641475 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493641475 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/935 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493641475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493641475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493641475 none C[C@@H](CC(N)=O)C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 11, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 32, 32, 45, 50, 50, 19, 19, 17, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 32, 32, 45, 45, 50, 50, 19, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 231 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/936 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493641475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493641475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493641475 none C[C@@H](CC(N)=O)C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 11, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 50, 50, 15, 15, 12, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 29, 29, 29, 48, 48, 50, 50, 15, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493641475 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475 Building ZINC001493641475 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493641475 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 935) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CC(N)=O)C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493641475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493641475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493641475 none C[C@@H](CC(N)=O)C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 11, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 32, 32, 45, 50, 50, 19, 19, 17, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 32, 32, 45, 45, 50, 50, 19, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 231 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 936) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](CC(N)=O)C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493641475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493641475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493641475 none C[C@@H](CC(N)=O)C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 11, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 50, 50, 15, 15, 12, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 29, 29, 29, 48, 48, 50, 50, 15, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493641475 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493641475 Building ZINC001493663642 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493663642 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/937 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493663642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493663642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493663642 none CN1C(=O)CC[C@H]1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 50, 34, 34, 15, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 34, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/938 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/938' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493663642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493663642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493663642 none CN1C(=O)CC[C@H]1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 37, 49, 33, 33, 19, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 10, 10, 49, 49, 49, 49, 49, 49, 49, 33, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493663642 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642 Building ZINC001493663642 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493663642 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 937) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493663642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493663642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493663642 none CN1C(=O)CC[C@H]1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 50, 34, 34, 15, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 34, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 938) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493663642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493663642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493663642 none CN1C(=O)CC[C@H]1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 37, 49, 33, 33, 19, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 10, 10, 49, 49, 49, 49, 49, 49, 49, 33, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493663642 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663642 Building ZINC001493663644 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493663644 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/939 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493663644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493663644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493663644 none CN1C(=O)CC[C@H]1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 34, 49, 28, 28, 14, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 49, 49, 49, 49, 49, 49, 49, 28, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/940 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493663644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493663644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493663644 none CN1C(=O)CC[C@H]1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 50, 32, 32, 14, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 6, 6, 50, 50, 50, 50, 50, 50, 50, 32, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493663644 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644 Building ZINC001493663644 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493663644 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 939) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493663644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493663644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493663644 none CN1C(=O)CC[C@H]1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 34, 49, 28, 28, 14, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 12, 12, 49, 49, 49, 49, 49, 49, 49, 28, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 940) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001493663644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493663644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001493663644 none CN1C(=O)CC[C@H]1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 50, 32, 32, 14, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 6, 6, 50, 50, 50, 50, 50, 50, 50, 32, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493663644 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493663644 Building ZINC001493671924 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493671924 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/941 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1) `ZINC001493671924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493671924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493671924 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 19, 39, 39, 39, 47, 47, 47, 50, 50, 47, 47, 47, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 39, 47, 50, 50, 47, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/942 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/942' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1) `ZINC001493671924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493671924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493671924 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 18, 41, 41, 41, 46, 46, 46, 50, 50, 46, 46, 46, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 41, 46, 50, 50, 46, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493671924 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924 Building ZINC001493671924 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493671924 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 941) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1) `ZINC001493671924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493671924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493671924 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 19, 39, 39, 39, 47, 47, 47, 50, 50, 47, 47, 47, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 39, 47, 50, 50, 47, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 942) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1) `ZINC001493671924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493671924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493671924 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 18, 41, 41, 41, 46, 46, 46, 50, 50, 46, 46, 46, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 41, 46, 50, 50, 46, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493671924 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671924 Building ZINC001493671926 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493671926 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/943 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1) `ZINC001493671926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493671926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493671926 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 22, 42, 42, 42, 47, 47, 47, 50, 50, 47, 47, 47, 8, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 42, 47, 50, 50, 47, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/944 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/944' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1) `ZINC001493671926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493671926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493671926 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 19, 41, 41, 41, 46, 46, 46, 50, 50, 46, 46, 46, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 41, 46, 50, 50, 46, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493671926 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926 Building ZINC001493671926 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493671926 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 943) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1) `ZINC001493671926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493671926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493671926 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 22, 42, 42, 42, 47, 47, 47, 50, 50, 47, 47, 47, 8, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 42, 47, 50, 50, 47, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 944) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1) `ZINC001493671926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493671926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001493671926 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc(C(N)=O)c[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 19, 41, 41, 41, 46, 46, 46, 50, 50, 46, 46, 46, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 41, 46, 50, 50, 46, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493671926 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493671926 Building ZINC001493697454 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493697454 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/945 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCn1cncn1)C1CC1) `ZINC001493697454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493697454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493697454 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 13, 17, 17, 17, 37, 27, 44, 50, 50, 50, 50, 7, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 17, 37, 37, 40, 40, 38, 42, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/946 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCn1cncn1)C1CC1) `ZINC001493697454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493697454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493697454 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 18, 18, 18, 37, 30, 43, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 18, 37, 37, 41, 41, 39, 39, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493697454 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454 Building ZINC001493697454 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493697454 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 945) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCn1cncn1)C1CC1) `ZINC001493697454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493697454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493697454 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 13, 17, 17, 17, 37, 27, 44, 50, 50, 50, 50, 7, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 17, 37, 37, 40, 40, 38, 42, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 946) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCn1cncn1)C1CC1) `ZINC001493697454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493697454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493697454 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCCn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 18, 18, 18, 37, 30, 43, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 18, 37, 37, 41, 41, 39, 39, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493697454 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697454 Building ZINC001493697438 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493697438 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/947 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCn1cncn1)C1CC1) `ZINC001493697438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493697438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493697438 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 21, 21, 21, 41, 33, 44, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 21, 41, 41, 43, 43, 39, 43, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/948 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCn1cncn1)C1CC1) `ZINC001493697438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493697438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493697438 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 11, 17, 17, 17, 44, 28, 46, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 17, 44, 44, 45, 45, 45, 40, 50, 50, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493697438 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438 Building ZINC001493697438 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493697438 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 947) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCn1cncn1)C1CC1) `ZINC001493697438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493697438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493697438 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 21, 21, 21, 41, 33, 44, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 21, 41, 41, 43, 43, 39, 43, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 948) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCn1cncn1)C1CC1) `ZINC001493697438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493697438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493697438 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCCn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 11, 17, 17, 17, 44, 28, 46, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 17, 44, 44, 45, 45, 45, 40, 50, 50, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493697438 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493697438 Building ZINC001493730333 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493730333 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/949 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1) `ZINC001493730333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493730333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493730333 none CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', '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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 4, 18, 28, 28, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/950 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/950' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1) `ZINC001493730333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493730333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493730333 none CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', '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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 4, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 16, 27, 27, 50, 50, 50, 50, 50, 16, 16, 16, 9, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493730333 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333 Building ZINC001493730333 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493730333 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 949) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1) `ZINC001493730333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493730333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493730333 none CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', '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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 4, 18, 28, 28, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 950) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1) `ZINC001493730333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493730333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493730333 none CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', '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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 4, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 16, 27, 27, 50, 50, 50, 50, 50, 16, 16, 16, 9, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493730333 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730333 Building ZINC001493730335 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493730335 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/951 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1) `ZINC001493730335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493730335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493730335 none CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', '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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 4, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 16, 27, 27, 50, 50, 50, 50, 50, 16, 16, 16, 9, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/952 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1) `ZINC001493730335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493730335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493730335 none CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', '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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 19, 29, 29, 50, 50, 50, 50, 50, 19, 19, 19, 9, 9, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493730335 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335 Building ZINC001493730335 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493730335 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 951) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1) `ZINC001493730335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493730335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493730335 none CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', '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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 4, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 16, 27, 27, 50, 50, 50, 50, 50, 16, 16, 16, 9, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 952) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1) `ZINC001493730335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493730335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493730335 none CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', '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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 9, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 19, 29, 29, 50, 50, 50, 50, 50, 19, 19, 19, 9, 9, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493730335 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493730335 Building ZINC001493821254 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493821254 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/953 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCS(C)(=O)=O)C1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493821254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493821254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493821254 none C[C@@H](NCCS(C)(=O)=O)C1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 14, 5, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 3, 13, 13, 20, 34, 34, 50, 50, 50, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 20, 34, 34, 34, 34, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 223 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/954 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/954' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCS(C)(=O)=O)C1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493821254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493821254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493821254 none C[C@@H](NCCS(C)(=O)=O)C1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 14, 5, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 19, 35, 35, 50, 50, 50, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 19, 35, 35, 35, 35, 50, 50, 50, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493821254 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254 Building ZINC001493821254 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493821254 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 953) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NCCS(C)(=O)=O)C1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493821254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493821254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493821254 none C[C@@H](NCCS(C)(=O)=O)C1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 14, 5, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 3, 13, 13, 20, 34, 34, 50, 50, 50, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 20, 34, 34, 34, 34, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 223 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 954) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NCCS(C)(=O)=O)C1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493821254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493821254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493821254 none C[C@@H](NCCS(C)(=O)=O)C1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 14, 5, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 19, 35, 35, 50, 50, 50, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 19, 35, 35, 35, 35, 50, 50, 50, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493821254 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821254 Building ZINC001493821257 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493821257 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/955 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCS(C)(=O)=O)C1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493821257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493821257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493821257 none C[C@H](NCCS(C)(=O)=O)C1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 14, 5, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 3, 14, 14, 20, 36, 36, 50, 50, 50, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 14, 14, 14, 20, 36, 36, 36, 36, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 224 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/956 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCS(C)(=O)=O)C1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493821257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493821257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493821257 none C[C@H](NCCS(C)(=O)=O)C1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 14, 5, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 20, 29, 29, 50, 50, 50, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 20, 29, 29, 29, 29, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 220 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493821257 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257 Building ZINC001493821257 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493821257 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 955) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NCCS(C)(=O)=O)C1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493821257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493821257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493821257 none C[C@H](NCCS(C)(=O)=O)C1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 14, 5, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 3, 14, 14, 20, 36, 36, 50, 50, 50, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 14, 14, 14, 20, 36, 36, 36, 36, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 224 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 956) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](NCCS(C)(=O)=O)C1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001493821257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493821257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493821257 none C[C@H](NCCS(C)(=O)=O)C1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 14, 5, 11, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 20, 29, 29, 50, 50, 50, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 20, 29, 29, 29, 29, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 220 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493821257 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493821257 Building ZINC001493835723 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493835723 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/957 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493835723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493835723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493835723 none C[C@@H](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 28, 28, 38, 50, 50, 50, 50, 50, 15, 15, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 28, 28, 28, 38, 38, 50, 50, 50, 50, 50, 15, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/958 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/958' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493835723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493835723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493835723 none C[C@@H](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 16, 27, 27, 37, 50, 50, 50, 50, 50, 16, 16, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 27, 27, 27, 37, 37, 50, 50, 50, 50, 50, 16, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493835723 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723 Building ZINC001493835723 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493835723 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 957) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493835723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493835723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493835723 none C[C@@H](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 28, 28, 38, 50, 50, 50, 50, 50, 15, 15, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 28, 28, 28, 38, 38, 50, 50, 50, 50, 50, 15, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 958) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493835723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493835723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493835723 none C[C@@H](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 16, 27, 27, 37, 50, 50, 50, 50, 50, 16, 16, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 27, 27, 27, 37, 37, 50, 50, 50, 50, 50, 16, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493835723 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835723 Building ZINC001493835724 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493835724 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/959 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493835724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493835724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493835724 none C[C@H](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 10, 25, 25, 37, 50, 50, 50, 50, 50, 10, 10, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 25, 25, 25, 37, 37, 50, 50, 50, 50, 50, 10, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/960 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/960' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493835724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493835724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493835724 none C[C@H](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 25, 25, 36, 50, 50, 50, 50, 50, 12, 12, 6, 6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 25, 25, 25, 36, 36, 50, 50, 50, 50, 50, 12, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493835724 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724 Building ZINC001493835724 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493835724 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 959) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493835724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493835724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493835724 none C[C@H](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 10, 25, 25, 37, 50, 50, 50, 50, 50, 10, 10, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 25, 25, 25, 37, 37, 50, 50, 50, 50, 50, 10, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 960) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493835724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493835724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493835724 none C[C@H](Cc1cnn(C)c1)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 25, 25, 36, 50, 50, 50, 50, 50, 12, 12, 6, 6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 25, 25, 25, 36, 36, 50, 50, 50, 50, 50, 12, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493835724 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835724 Building ZINC001493835738 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493835738 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/961 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC2CCOCC2)C1) `ZINC001493835738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493835738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493835738 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 7, 7, 7, 22, 49, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/962 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/962' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC2CCOCC2)C1) `ZINC001493835738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493835738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493835738 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 21, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493835738 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738 Building ZINC001493835738 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493835738 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 961) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CC[C@H](NC(=O)COC2CCOCC2)C1) `ZINC001493835738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493835738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493835738 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 7, 7, 7, 22, 49, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 962) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CC[C@H](NC(=O)COC2CCOCC2)C1) `ZINC001493835738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493835738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001493835738 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 21, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493835738 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493835738 Building ZINC001493836661 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493836661 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/963 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493836661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493836661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001493836661 none CCC[C@@H](NC(N)=O)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 12, 35, 35, 40, 40, 40, 12, 12, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 12, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/964 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/964' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493836661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493836661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001493836661 none CCC[C@@H](NC(N)=O)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 33, 11, 33, 33, 38, 38, 38, 11, 11, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 49, 49, 49, 49, 49, 49, 49, 38, 38, 38, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493836661 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661 Building ZINC001493836661 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493836661 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 963) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493836661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493836661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001493836661 none CCC[C@@H](NC(N)=O)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 12, 35, 35, 40, 40, 40, 12, 12, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 12, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 964) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493836661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493836661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001493836661 none CCC[C@@H](NC(N)=O)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 33, 11, 33, 33, 38, 38, 38, 11, 11, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 49, 49, 49, 49, 49, 49, 49, 38, 38, 38, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493836661 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836661 Building ZINC001493836674 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493836674 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/965 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CNC(=O)c2ccco2)C1) `ZINC001493836674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493836674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001493836674 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CNC(=O)c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 23, 41, 42, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 23, 23, 42, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47] set([39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/966 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/966' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CNC(=O)c2ccco2)C1) `ZINC001493836674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493836674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001493836674 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CNC(=O)c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 45, 45, 45, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 25, 25, 45, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493836674 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674 Building ZINC001493836674 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493836674 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 965) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CC[C@H](NC(=O)CNC(=O)c2ccco2)C1) `ZINC001493836674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493836674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001493836674 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CNC(=O)c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 23, 41, 42, 41, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 23, 23, 42, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47] set([39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 966) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CC[C@H](NC(=O)CNC(=O)c2ccco2)C1) `ZINC001493836674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493836674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001493836674 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CNC(=O)c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 45, 45, 45, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 25, 25, 45, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493836674 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493836674 Building ZINC001493840140 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493840140 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/967 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CNC(=O)C2CCC2)C1) `ZINC001493840140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493840140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493840140 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CNC(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 15, 26, 27, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 27, 50, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 49, 50] set([48, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/83982/xcb-8058097.54/working/building/ZINC001493840140 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/968 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/968' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CNC(=O)C2CCC2)C1) `ZINC001493840140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493840140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493840140 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CNC(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 5, 5, 5, 18, 24, 24, 24, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 18, 18, 24, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493840140 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140 Building ZINC001493840140 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493840140 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 967) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CC[C@H](NC(=O)CNC(=O)C2CCC2)C1) `ZINC001493840140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493840140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493840140 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CNC(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 15, 26, 27, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 27, 50, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 49, 50] set([48, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/83982/xcb-8058097.54/working/building/ZINC001493840140 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 968) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N1CC[C@H](NC(=O)CNC(=O)C2CCC2)C1) `ZINC001493840140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493840140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493840140 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CNC(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 5, 5, 5, 18, 24, 24, 24, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 18, 18, 24, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493840140 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493840140 Building ZINC001493868213 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493868213 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/969 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCN2CCCC2=O)C1) `ZINC001493868213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493868213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493868213 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 17, 18, 18, 18, 18, 18, 18, 37, 37, 50, 50, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/970 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/970' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCN2CCCC2=O)C1) `ZINC001493868213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493868213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493868213 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 17, 17, 17, 17, 17, 17, 36, 36, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493868213 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213 Building ZINC001493868213 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493868213 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 969) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCN2CCCC2=O)C1) `ZINC001493868213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493868213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493868213 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 17, 18, 18, 18, 18, 18, 18, 37, 37, 50, 50, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 970) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCN2CCCC2=O)C1) `ZINC001493868213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493868213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493868213 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 17, 17, 17, 17, 17, 17, 36, 36, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493868213 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868213 Building ZINC001493868300 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493868300 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/971 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2cccn2)C1) `ZINC001493868300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493868300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493868300 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 7, 7, 25, 26, 45, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 32, 32, 41, 42, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/972 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/972' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2cccn2)C1) `ZINC001493868300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493868300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493868300 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 11, 11, 29, 30, 47, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 29, 29, 36, 36, 43, 46, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493868300 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300 Building ZINC001493868300 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493868300 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 971) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2cccn2)C1) `ZINC001493868300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493868300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493868300 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 7, 7, 25, 26, 45, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 32, 32, 41, 42, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 972) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2cccn2)C1) `ZINC001493868300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493868300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493868300 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 11, 11, 29, 30, 47, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 29, 29, 36, 36, 43, 46, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493868300 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493868300 Building ZINC001493869082 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493869082 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/973 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001493869082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493869082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493869082 none CCn1ccc(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 24, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 32, 50, 50, 50, 50, 50, 32, 32, 24, 24, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/974 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/974' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001493869082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493869082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493869082 none CCn1ccc(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 24, 9, 8, 9, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 32, 50, 50, 50, 50, 50, 32, 32, 24, 24, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493869082 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082 Building ZINC001493869082 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493869082 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 973) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001493869082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493869082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493869082 none CCn1ccc(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 24, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 32, 50, 50, 50, 50, 50, 32, 32, 24, 24, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 974) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001493869082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493869082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493869082 none CCn1ccc(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 24, 9, 8, 9, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 32, 50, 50, 50, 50, 50, 32, 32, 24, 24, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493869082 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493869082 Building ZINC001493876338 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493876338 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/975 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCn2ccccc2=O)C1) `ZINC001493876338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493876338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493876338 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 16, 16, 38, 41, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 38, 38, 41, 41, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/976 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/976' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCn2ccccc2=O)C1) `ZINC001493876338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493876338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493876338 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 15, 15, 36, 40, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 36, 36, 40, 40, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493876338 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338 Building ZINC001493876338 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493876338 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 975) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCn2ccccc2=O)C1) `ZINC001493876338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493876338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493876338 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 16, 16, 38, 41, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 38, 38, 41, 41, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 976) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCn2ccccc2=O)C1) `ZINC001493876338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493876338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001493876338 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 15, 15, 36, 40, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 36, 36, 40, 40, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493876338 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876338 Building ZINC001493876500 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493876500 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/977 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001493876500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493876500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493876500 none CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 27, 9, 27, 8, 9, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 27] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/978 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/978' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001493876500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493876500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493876500 none CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 27, 9, 27, 8, 9, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 27] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493876500 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500 Building ZINC001493876500 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493876500 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 977) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001493876500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493876500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493876500 none CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 27, 9, 27, 8, 9, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 27] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 978) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001493876500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493876500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493876500 none CCN1C[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 27, 9, 27, 8, 9, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 27] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493876500 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876500 Building ZINC001493876501 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493876501 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/979 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001493876501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493876501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493876501 none CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/980 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/980' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001493876501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493876501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493876501 none CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 10, 28, 9, 10, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493876501 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501 Building ZINC001493876501 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493876501 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 979) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001493876501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493876501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493876501 none CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 10, 28, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 980) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001493876501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493876501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001493876501 none CCN1C[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', '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.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 10, 28, 9, 10, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493876501 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493876501 Building ZINC001493890421 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493890421 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/981 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@]2(C)CCNC(=O)C2)C1) `ZINC001493890421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493890421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493890421 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@]2(C)CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 28, 46, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/982 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/982' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@]2(C)CCNC(=O)C2)C1) `ZINC001493890421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493890421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493890421 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@]2(C)CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 17, 30, 42, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 133 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493890421 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421 Building ZINC001493890421 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493890421 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 981) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@]2(C)CCNC(=O)C2)C1) `ZINC001493890421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493890421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493890421 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@]2(C)CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 28, 46, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 982) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@]2(C)CCNC(=O)C2)C1) `ZINC001493890421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493890421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493890421 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@]2(C)CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 17, 30, 42, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 133 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493890421 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890421 Building ZINC001493890422 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493890422 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/983 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]2(C)CCNC(=O)C2)C1) `ZINC001493890422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493890422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493890422 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]2(C)CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [2, 1, 2, 2, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 31, 46, 50, 50, 50, 50, 50, 50, 50, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 134 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/984 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/984' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]2(C)CCNC(=O)C2)C1) `ZINC001493890422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493890422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493890422 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]2(C)CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 21, 21, 21, 21, 21, 36, 47, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 128 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493890422 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422 Building ZINC001493890422 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493890422 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 983) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]2(C)CCNC(=O)C2)C1) `ZINC001493890422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493890422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493890422 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]2(C)CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [2, 1, 2, 2, 1, 1, 1, 3, 3, 6, 14, 14, 14, 14, 14, 31, 46, 50, 50, 50, 50, 50, 50, 50, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 134 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 984) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]2(C)CCNC(=O)C2)C1) `ZINC001493890422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493890422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001493890422 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]2(C)CCNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 21, 21, 21, 21, 21, 36, 47, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 128 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493890422 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493890422 Building ZINC001493902857 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493902857 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/985 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cn3cccnc3n2)C1) `ZINC001493902857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493902857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493902857 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cn3cccnc3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/986 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/986' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cn3cccnc3n2)C1) `ZINC001493902857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493902857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493902857 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cn3cccnc3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493902857 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857 Building ZINC001493902857 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493902857 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 985) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cn3cccnc3n2)C1) `ZINC001493902857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493902857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493902857 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cn3cccnc3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 986) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cn3cccnc3n2)C1) `ZINC001493902857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493902857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001493902857 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cn3cccnc3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493902857 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493902857 Building ZINC001493906260 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493906260 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/987 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493906260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493906260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493906260 none CCCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 21, 27, 20, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 27, 21, 21, 20, 20, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/988 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/988' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493906260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493906260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493906260 none CCCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 20, 27, 19, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 27, 20, 20, 19, 19, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493906260 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260 Building ZINC001493906260 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493906260 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 987) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493906260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493906260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493906260 none CCCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 21, 27, 20, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 27, 21, 21, 20, 20, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 988) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493906260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493906260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001493906260 none CCCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 20, 27, 19, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 27, 20, 20, 19, 19, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 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, 38, 39, 40, 41, 51, 52]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493906260 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493906260 Building ZINC001493910642 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493910642 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/989 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001493910642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493910642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493910642 none CNC(=O)C1(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 32, 13, 32, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 42, 42, 42, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/990 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/990' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001493910642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493910642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493910642 none CNC(=O)C1(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 38, 13, 38, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 45, 45, 45, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493910642 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642 Building ZINC001493910642 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493910642 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 989) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001493910642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493910642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493910642 none CNC(=O)C1(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 32, 13, 32, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 42, 42, 42, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 990) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1) `ZINC001493910642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493910642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001493910642 none CNC(=O)C1(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 38, 13, 38, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 45, 45, 45, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493910642 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493910642 Building ZINC001493911585 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493911585 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/991 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001493911585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493911585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493911585 none COc1c(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 15, 26, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/992 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/992' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001493911585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493911585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493911585 none COc1c(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 14, 27, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493911585 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585 Building ZINC001493911585 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493911585 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 991) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001493911585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493911585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493911585 none COc1c(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 15, 26, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 992) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001493911585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493911585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001493911585 none COc1c(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 14, 27, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493911585 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493911585 Building ZINC001493916642 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493916642 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/993 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493916642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493916642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493916642 none Cn1ccnc1CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 37, 14, 11, 14, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 38, 38, 37, 37, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/994 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/994' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493916642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493916642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493916642 none Cn1ccnc1CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 35, 14, 11, 14, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 35, 35, 35, 35, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493916642 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642 Building ZINC001493916642 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493916642 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 993) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493916642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493916642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493916642 none Cn1ccnc1CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 37, 14, 11, 14, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 38, 38, 37, 37, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 994) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493916642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493916642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493916642 none Cn1ccnc1CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 35, 14, 11, 14, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 35, 35, 35, 35, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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, 38, 48, 49]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493916642 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493916642 Building ZINC001493922887 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493922887 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/995 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccnc1CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493922887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493922887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493922887 none COc1cccnc1CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 7, 6, 7, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 34, 34, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/996 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/996' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccnc1CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493922887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493922887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493922887 none COc1cccnc1CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 10, 8, 10, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 35, 35, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493922887 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887 Building ZINC001493922887 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001493922887 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 995) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccnc1CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493922887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493922887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493922887 none COc1cccnc1CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 7, 6, 7, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 34, 34, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 996) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccnc1CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001493922887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493922887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001493922887 none COc1cccnc1CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 10, 8, 10, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 35, 35, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493922887 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887/0.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493922887 Building ZINC001493942174 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493942174 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/997 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 23, 33, 33, 33, 46, 46, 13, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 99, 46, 46, 46, 46, 46, 13, 13] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 338 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/998 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/998' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 23, 33, 33, 33, 46, 46, 13, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 99, 46, 46, 46, 46, 46, 13, 13] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 338 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/999 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/999' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 19, 32, 32, 32, 45, 45, 8, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 96, 45, 45, 45, 45, 45, 8, 8] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 318 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/83982/xcb-8058097.54/working/3D/1000 `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/1000' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 19, 32, 32, 32, 45, 45, 8, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 96, 45, 45, 45, 45, 45, 8, 8] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 318 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493942174 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 Building ZINC001493942174 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493942174 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 997) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 23, 33, 33, 33, 46, 46, 13, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 99, 46, 46, 46, 46, 46, 13, 13] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 338 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 998) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 23, 33, 33, 33, 46, 46, 13, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 99, 46, 46, 46, 46, 46, 13, 13] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 338 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 999) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 19, 32, 32, 32, 45, 45, 8, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 96, 45, 45, 45, 45, 45, 8, 8] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 318 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 1000) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/1000: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 19, 32, 32, 32, 45, 45, 8, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 96, 45, 45, 45, 45, 45, 8, 8] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 318 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493942174 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 Building ZINC001493942174 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493942174 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 997) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 23, 33, 33, 33, 46, 46, 13, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 99, 46, 46, 46, 46, 46, 13, 13] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 338 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 998) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 23, 33, 33, 33, 46, 46, 13, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 99, 46, 46, 46, 46, 46, 13, 13] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 338 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 999) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 19, 32, 32, 32, 45, 45, 8, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 96, 45, 45, 45, 45, 45, 8, 8] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 318 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 1000) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/1000: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 19, 32, 32, 32, 45, 45, 8, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 96, 45, 45, 45, 45, 45, 8, 8] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 318 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493942174 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 Building ZINC001493942174 mkdir: created directory `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001493942174 mkdir: created directory `0' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/0 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 0 (index: 997) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 23, 33, 33, 33, 46, 46, 13, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 99, 46, 46, 46, 46, 46, 13, 13] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 338 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `1' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/1 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 1 (index: 998) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 7, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 23, 33, 33, 33, 46, 46, 13, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 99, 46, 46, 46, 46, 46, 13, 13] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 338 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `2' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/2 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 2 (index: 999) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 19, 32, 32, 32, 45, 45, 8, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 96, 45, 45, 45, 45, 45, 8, 8] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 318 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 mkdir: created directory `3' /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/3 /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Protomer 3 (index: 1000) grep: /scratch/xiaobo/83982/xcb-8058097.54/working/3D/1000: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1) `ZINC001493942174.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001493942174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001493942174 none CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C[C@H](O)COC)C1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 10, 5, 5, 7, 12, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 19, 32, 32, 32, 45, 45, 8, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 96, 45, 45, 45, 45, 45, 8, 8] 150 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 318 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Finished preparing ZINC001493942174 Recording results /scratch/xiaobo/83982/xcb-8058097.54/working /scratch/xiaobo/83982/xcb-8058097.54 Appending to /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.* 0: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/0.* 3: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/3.* 2: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/2.* 1: /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174/1.* Removing working files in /scratch/xiaobo/83982/xcb-8058097.54/working/building/ZINC001493942174 /scratch/xiaobo/83982/xcb-8058097.54 Compressing combined databse files /scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/83982/xcb-8058097.54/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/83982/xcb-8058097.54/working/3D/1001' removed directory: `/scratch/xiaobo/83982/xcb-8058097.54/working/3D' rmdir: removing directory, `/scratch/xiaobo/83982/xcb-8058097.54/working/building' rmdir: removing directory, `/scratch/xiaobo/83982/xcb-8058097.54/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/logs `/scratch/xiaobo/83982/xcb-8058097.54' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xcb' `/scratch/xiaobo/83982/xcb-8058097.54/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xcb/finished' `/scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xcb/finished/xcb.db2.gz' removed `/scratch/xiaobo/83982/xcb-8058097.54/finished/xcb.db2.gz' removed directory: `/scratch/xiaobo/83982/xcb-8058097.54/finished' removed directory: `/scratch/xiaobo/83982/xcb-8058097.54'